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This page was generated on 2025-03-17 12:08 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4756
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4487
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4514
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4441
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4399
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: 2025-03-13 13:00 -0400 (Thu, 13 Mar 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 -0400 (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: 2025-03-13 23:54:35 -0400 (Thu, 13 Mar 2025)
EndedAt: 2025-03-13 23:58:21 -0400 (Thu, 13 Mar 2025)
EllapsedTime: 225.6 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 4.669  1.255   6.875
* 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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-03-13 23:56:08.833][biodb::testContext]
biodb.INFO [2025-03-13 23:56:08.851][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-13 23:56:08.854][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-13 23:56:08.858][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-13 23:56:08.871][biodb::testContext]
biodb.INFO [2025-03-13 23:56:08.886][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-13 23:56:08.909][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-13 23:56:08.948][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 23:56:08.952][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-13 23:56:08.956][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-13 23:56:08.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:08.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:08.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:08.987][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-13 23:56:09.155][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-13 23:56:09.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:09.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:09.161][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[2025-03-13 23:56:09.173][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-13 23:56:09.175][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-13 23:56:09.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:09.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:09.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:09.192][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-13 23:56:09.195][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-13 23:56:09.198][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-13 23:56:09.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:09.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:09.214][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[2025-03-13 23:56:09.216][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-13 23:56:09.218][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-13 23:56:09.230][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-13 23:56:09.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:09.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:09.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:09.239][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-13 23:56:09.250][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-13 23:56:09.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:09.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:09.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:09.266][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-13 23:56:09.269][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-13 23:56:09.272][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-13 23:56:09.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:09.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:09.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:09.290][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-13 23:56:09.292][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-13 23:56:09.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:09.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:09.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:09.311][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-13 23:56:09.313][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-13 23:56:09.315][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-13 23:56:09.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:09.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:09.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:09.334][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-13 23:56:09.346][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-13 23:56:09.349][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-13 23:56:09.351][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-13 23:56:09.353][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-13 23:56:09.366][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-13 23:56:09.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:09.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:09.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:09.375][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-13 23:56:09.385][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-13 23:56:09.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:09.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:09.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:09.394][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-13 23:56:09.406][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-13 23:56:09.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:09.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:09.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:09.425][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-13 23:56:09.427][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-13 23:56:09.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:09.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:09.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:09.446][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-13 23:56:09.449][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-13 23:56:09.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:09.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:09.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:09.462][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-13 23:56:09.465][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-13 23:56:09.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:09.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:09.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:09.485][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-13 23:56:09.488][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-13 23:56:09.510][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-13 23:56:09.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:09.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:09.517][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[2025-03-13 23:56:09.522][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-13 23:56:09.524][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-13 23:56:09.527][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-13 23:56:09.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:09.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:09.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:09.549][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-13 23:56:09.721][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:56:09.806][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-13 23:56:09.809][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:09.811][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:56:09.823][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:09.825][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:56:09.827][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 23:56:09.829][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 23:56:09.840][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-13 23:56:09.843][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:56:09.845][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:09.847][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-13 23:56:09.849][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:56:09.863][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:56:09.865][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:09.868][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 23:56:09.868][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-13 23:56:09.868][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-13 23:56:09.868][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-13 23:56:09.868][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-13 23:56:09.870][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 23:56:09.883][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:56:09.885][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:56:09.887][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:56:09.890][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:56:09.909][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:56:09.921][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:56:09.924][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:56:09.926][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:56:09.928][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:56:09.940][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 23:56:09.942][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:56:09.945][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-13 23:56:09.949][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:56:09.962][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-13 23:56:09.964][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:09.966][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:56:09.968][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:09.980][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:56:09.983][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 23:56:09.985][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 23:56:09.987][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-13 23:56:09.989][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:56:10.011][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:10.013][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-13 23:56:10.016][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:56:10.018][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:56:10.031][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:10.034][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 23:56:10.034][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-13 23:56:10.034][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-13 23:56:10.034][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-13 23:56:10.034][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-13 23:56:10.037][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 23:56:10.039][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:56:10.050][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:56:10.053][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:56:10.055][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:56:10.057][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:56:10.059][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:56:10.070][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:56:10.072][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:56:10.074][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:56:10.076][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 23:56:10.088][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:56:10.091][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-13 23:56:10.095][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:10.108][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-13 23:56:10.111][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:10.113][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:56:10.115][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:10.118][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:56:10.129][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 23:56:10.131][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 23:56:10.133][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-13 23:56:10.136][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:56:10.144][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:56:10.147][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-13 23:56:10.149][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:56:10.151][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:56:10.163][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:10.165][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:56:10.168][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 23:56:10.170][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:56:10.181][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:56:10.184][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:56:10.186][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:56:10.188][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:56:10.190][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:56:10.201][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:56:10.203][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:56:10.205][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:56:10.208][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 23:56:10.217][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:56:10.220][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-13 23:56:10.224][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:10.237][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-13 23:56:10.240][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:10.242][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:56:10.244][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:10.247][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:56:10.260][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 23:56:10.262][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 23:56:10.265][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-13 23:56:10.267][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:56:10.279][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:56:10.281][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-13 23:56:10.283][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:56:10.286][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:56:10.300][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:10.302][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:56:10.304][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 23:56:10.307][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:56:10.323][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:56:10.325][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:56:10.327][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:56:10.329][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:56:10.331][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:56:10.343][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:56:10.345][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:56:10.347][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:56:10.349][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 23:56:10.365][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:56:10.372][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 23:56:10.374][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:10.385][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[2025-03-13 23:56:10.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:10.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:10.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:10.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:10.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:10.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:10.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:10.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:10.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:10.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:10.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:10.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:10.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:10.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:10.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:10.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:10.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:10.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:10.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:10.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:10.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:10.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:10.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:10.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:10.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:10.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:10.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:10.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:10.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:10.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:10.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:10.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:10.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:10.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:10.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:10.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:10.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:10.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:10.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:10.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:10.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:10.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:10.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:10.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:10.576][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[2025-03-13 23:56:10.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:10.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:10.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:10.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:10.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:10.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:10.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:10.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:10.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:10.607][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[2025-03-13 23:56:10.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:10.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:10.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:10.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:10.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:10.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:10.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:10.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:10.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:10.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:10.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:10.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:10.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:10.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:10.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:10.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:10.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:10.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:10.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:10.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:10.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:10.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:10.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:10.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:10.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:10.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:10.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:10.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:10.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:10.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:10.760][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-13 23:56:10.778][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-13 23:56:10.781][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-13 23:56:10.784][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-13 23:56:10.797][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-13 23:56:10.800][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-13 23:56:10.804][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-13 23:56:10.818][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-13 23:56:10.821][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-13 23:56:10.824][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-13 23:56:10.838][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-13 23:56:10.842][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-13 23:56:10.845][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-13 23:56:10.858][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-13 23:56:10.861][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-13 23:56:10.864][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-13 23:56:10.879][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-13 23:56:10.882][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-13 23:56:10.886][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-13 23:56:10.898][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-13 23:56:10.901][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-13 23:56:10.905][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-13 23:56:10.916][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-13 23:56:10.920][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-13 23:56:10.923][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-13 23:56:10.934][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-13 23:56:10.937][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-13 23:56:10.940][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-13 23:56:10.954][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-13 23:56:10.957][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-13 23:56:10.960][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-13 23:56:10.973][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-13 23:56:10.976][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-13 23:56:10.980][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-13 23:56:10.983][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-13 23:56:10.986][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-13 23:56:10.989][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-13 23:56:11.015][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-13 23:56:11.018][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-13 23:56:11.022][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-13 23:56:11.035][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-13 23:56:11.038][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-13 23:56:11.049][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-13 23:56:11.053][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-13 23:56:11.056][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-13 23:56:11.070][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-13 23:56:11.074][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-13 23:56:11.078][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-13 23:56:11.090][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-13 23:56:11.094][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-13 23:56:11.097][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-13 23:56:11.110][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-13 23:56:11.114][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-13 23:56:11.117][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-13 23:56:11.127][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-13 23:56:11.131][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-13 23:56:11.134][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-13 23:56:11.151][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-13 23:56:11.154][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-13 23:56:11.158][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-13 23:56:11.171][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-13 23:56:11.175][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-13 23:56:11.187][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-13 23:56:11.192][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-13 23:56:11.195][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-13 23:56:11.215][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-13 23:56:11.220][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-13 23:56:11.223][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-13 23:56:11.238][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-13 23:56:11.242][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-13 23:56:11.245][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-13 23:56:11.259][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-13 23:56:11.262][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-13 23:56:11.273][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-13 23:56:11.277][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-13 23:56:11.280][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-13 23:56:11.295][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-13 23:56:11.299][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-13 23:56:11.303][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-13 23:56:11.316][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-13 23:56:11.319][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-13 23:56:11.323][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-13 23:56:11.336][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-13 23:56:11.361][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-13 23:56:11.374][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-13 23:56:11.380][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 23:56:11.393][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:11.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:11.398][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:11.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:11.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:11.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:11.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:11.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:11.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:11.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:11.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:11.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:11.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:11.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:11.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:11.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:11.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:11.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:11.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:11.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:11.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:11.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:11.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:11.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:11.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:11.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:11.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:11.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:11.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:11.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:11.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:11.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:11.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:11.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:11.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:11.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:11.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:11.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:11.568][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[2025-03-13 23:56:11.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:11.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:11.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:11.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:11.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:11.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:11.610][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.DEBUG[2025-03-13 23:56:11.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:11.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:11.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:11.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:11.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:11.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:11.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:11.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:11.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:11.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:11.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:11.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:11.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:11.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:11.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:11.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:11.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:11.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:11.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:11.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:11.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:11.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:11.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:11.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:11.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:11.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:11.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:11.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:11.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:11.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:11.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:11.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:11.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:11.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:11.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:11.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:11.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:11.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:11.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:11.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:11.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:11.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:11.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:11.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:11.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:11.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:11.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:11.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:11.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:11.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:11.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:11.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:11.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:11.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:11.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:11.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:11.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:11.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:11.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:11.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:11.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:11.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:11.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:11.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:11.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:11.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:11.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:11.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:11.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:11.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:11.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:56:11.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:11.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:11.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:11.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:11.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:11.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:11.927][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-13 23:56:11.982][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-13 23:56:11.986][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:56:11.993][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-13 23:56:11.995][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:11.997][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:56:11.999][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:12.001][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:56:12.014][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:12.017][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-13 23:56:12.019][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-13 23:56:12.021][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:56:12.033][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:12.036][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-13 23:56:12.038][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:56:12.040][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-13 23:56:12.040][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-13 23:56:12.040][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-13 23:56:12.040][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-13 23:56:12.040][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-13 23:56:12.040][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-13 23:56:12.040][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-13 23:56:12.040][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-13 23:56:12.040][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-13 23:56:12.040][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-13 23:56:12.040][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-13 23:56:12.057][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-13 23:56:12.060][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 23:56:12.060][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-13 23:56:12.060][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-13 23:56:12.062][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-13 23:56:12.064][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:56:12.076][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:56:12.080][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:56:12.082][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:56:12.084][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:56:12.086][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:56:12.099][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:56:12.099][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-13 23:56:12.101][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:56:12.103][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:56:12.106][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-13 23:56:12.122][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-13 23:56:12.122][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-13 23:56:12.155][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-13 23:56:12.168][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-13 23:56:12.171][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-13 23:56:12.175][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-13 23:56:12.191][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-13 23:56:12.195][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-13 23:56:12.287][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-13 23:56:12.290][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-13 23:56:12.304][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-13 23:56:12.321][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-13 23:56:12.329][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 23:56:12.343][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 23:56:12.346][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-13 23:56:12.349][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-13 23:56:12.384][biodb::testThat]
biodb.INFO [2025-03-13 23:56:12.386][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-13 23:56:12.388][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:56:12.400][biodb::testThat]
biodb.TRACE[2025-03-13 23:56:12.412][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[2025-03-13 23:56:12.436][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:56:12.452][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:56:12.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:12.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:12.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:12.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:12.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:12.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:12.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:56:12.587][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:12.590][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:12.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:12.594][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:12.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:12.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:12.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:12.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:12.685][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:12.688][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:12.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:12.703][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:12.847][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:12.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:12.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:12.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:12.865][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:12.878][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:12.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:12.883][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:12.886][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:12.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:12.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:12.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:12.905][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:12.915][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:12.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:12.919][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:12.922][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:12.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:12.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:12.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:12.940][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:12.942][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:12.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:12.959][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:12.961][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:12.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:12.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:12.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:12.980][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:12.983][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:12.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.002][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.005][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:13.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:13.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.024][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:13.036][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:13.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.041][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.044][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:13.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:13.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.064][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:13.076][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:13.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.081][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:13.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:13.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.104][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:13.117][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:13.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.122][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.125][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:13.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:13.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.146][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:13.240][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:13.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.254][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.257][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:13.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:13.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.276][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:13.279][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:13.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.292][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.296][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:13.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:13.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:13.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:13.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:13.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:13.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:13.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:13.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:13.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:13.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:13.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:13.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:13.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:13.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:13.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:13.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:13.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:13.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:13.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:13.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:13.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:13.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:13.700][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-03-13 23:56:13.705][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:13.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:13.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.725][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:13.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:13.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.876][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:13.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:13.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:13.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:13.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.933][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:13.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:13.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:13.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:13.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.973][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-13 23:56:13.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-13 23:56:13.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:13.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:13.993][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-13 23:56:13.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-13 23:56:13.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.013][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-13 23:56:14.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-13 23:56:14.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.022][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-13 23:56:14.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-13 23:56:14.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:14.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:14.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:14.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:14.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:14.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:14.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:14.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:14.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:14.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:14.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:14.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:14.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:14.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:14.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:14.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:14.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:14.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:14.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:14.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:14.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:14.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:14.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:14.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:14.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:14.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:14.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:14.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:14.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.541][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:14.543][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:14.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.547][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:14.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:14.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:14.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:14.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:14.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:14.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:14.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:14.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.694][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:14.697][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:14.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.709][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:14.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:14.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:14.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:14.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:14.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:14.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.808][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:14.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:14.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.826][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:14.829][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:14.831][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.833][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.846][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:14.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:14.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.905][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:14.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:14.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.927][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:14.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:14.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.947][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:14.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:14.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.966][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:14.968][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:14.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.973][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:14.985][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:14.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:14.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:14.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:15.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:15.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:15.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:15.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:15.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:15.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.094][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:15.107][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:15.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.111][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.114][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:15.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:15.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:15.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:15.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:15.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:15.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:15.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:15.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.230][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:15.244][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:15.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.249][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:15.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:15.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.307][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:15.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:15.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.347][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:15.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:15.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.367][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:15.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:15.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.395][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:15.397][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:15.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.412][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.414][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:15.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:15.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.474][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-13 23:56:15.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:15.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.497][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-13 23:56:15.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:15.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.518][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-13 23:56:15.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:15.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.550][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-13 23:56:15.552][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:15.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.568][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.571][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-13 23:56:15.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:15.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.657][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:15.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:15.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.690][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:15.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:15.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.706][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:15.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:15.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.724][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:15.727][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:15.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.731][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.741][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:15.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:15.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.802][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:15.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:15.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.825][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:15.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:15.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.848][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:15.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:15.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.868][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:15.870][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:15.873][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.875][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.887][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:15.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:15.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.938][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:15.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:15.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.969][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:15.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:15.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:15.991][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:15.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:15.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:15.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:16.015][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:16.018][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:16.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:16.033][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:16.037][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:16.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:16.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:16.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:16.096][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:16.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:16.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:16.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:16.117][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:16.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:16.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:16.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:16.180][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:16.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:16.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:16.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:16.204][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:16.207][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:16.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:16.223][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:16.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:16.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:16.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:16.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:16.299][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:16.302][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:16.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:16.307][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:16.336][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:16.338][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:16.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:16.344][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:16.377][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:16.380][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:16.382][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:16.384][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:16.406][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:16.420][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:16.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:16.424][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:16.455][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:16.458][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:16.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:16.475][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:16.497][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:16.500][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:16.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:16.504][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:16.536][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:16.538][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:16.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:16.543][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:16.565][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:16.581][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:16.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:16.586][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:16.609][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-13 23:56:16.627][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:16.629][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:16.631][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:16.651][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:16.654][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:16.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:16.680][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:16.700][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:16.703][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:16.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:16.719][ef$get] fields variable is a list.
biodb.INFO [2025-03-13 23:56:16.758][biodb::testThat]
biodb.INFO [2025-03-13 23:56:16.760][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-13 23:56:16.762][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:56:16.774][biodb::testThat]
biodb.DEBUG[2025-03-13 23:56:16.842][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-03-13 23:56:16.879][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:56:16.889][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-03-13 23:56:16.902][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:56:16.906][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-03-13 23:56:16.908][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:56:17.068][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:56:17.071][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:56:17.075][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:17.088][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:17.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:17.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:17.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:17.119][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:17.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:56:17.138][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:17.150][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:17.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.155][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:17.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:17.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.287][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:17.300][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:17.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.305][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.308][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:17.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:17.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.341][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:17.345][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:17.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.350][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.364][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:17.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:17.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.386][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:17.389][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:17.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.405][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:17.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:17.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.432][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:17.445][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:17.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.451][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.464][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:17.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:17.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.488][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:17.491][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:17.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.506][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.509][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:17.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:17.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.531][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:17.549][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:17.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.554][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.567][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:17.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:17.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.588][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:17.592][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:17.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.606][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:17.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:17.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.632][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:17.635][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:17.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.668][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:17.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:17.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.707][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:17.710][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:17.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.715][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.728][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:17.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:17.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.750][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:17.753][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:17.764][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.767][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.770][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:17.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:17.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:17.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:17.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:17.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:17.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:17.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:17.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:17.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:17.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:17.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:17.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:17.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:17.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:17.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:17.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:17.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:17.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:17.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:17.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:18.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:18.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:18.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:18.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:18.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:18.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:18.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:18.051][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-03-13 23:56:18.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-13 23:56:18.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-13 23:56:18.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:18.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:18.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-13 23:56:18.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-13 23:56:18.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:18.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:18.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-13 23:56:18.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-13 23:56:18.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:18.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-13 23:56:18.171][biodb::testThat]
biodb.INFO [2025-03-13 23:56:18.174][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-13 23:56:18.178][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:56:18.192][biodb::testThat]
biodb.TRACE[2025-03-13 23:56:18.202][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:18.215][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:18.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:18.232][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:18.235][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-03-13 23:56:18.394][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:18.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:18.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:18.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:18.412][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:18.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:18.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:18.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:18.429][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:18.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:18.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:18.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:18.469][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-03-13 23:56:18.488][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-13 23:56:18.602][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:56:18.680][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-13 23:56:18.692][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:56:18.696][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-13 23:56:18.819][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[2025-03-13 23:56:18.836][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:56:18.838][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:56:18.849][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-13 23:56:19.986][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-13 23:56:20.545][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:56:20.550][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-13 23:56:20.588][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-13 23:56:20.619][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-03-13 23:56:20.647][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:20.650][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:20.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:20.654][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:20.656][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:20.658][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:20.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:20.676][ef$get] fields variable is a list.
biodb.INFO [2025-03-13 23:56:20.685][biodb::testThat]
biodb.INFO [2025-03-13 23:56:20.688][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-13 23:56:20.690][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:56:20.692][biodb::testThat]
biodb.TRACE[2025-03-13 23:56:20.777][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:20.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:20.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:20.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:20.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:20.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:20.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:20.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:20.813][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:20.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:20.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:20.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:21.152][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:56:21.160][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:56:21.172][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-13 23:56:21.175][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:56:21.179][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-03-13 23:56:21.255][biodb::testThat]
biodb.INFO [2025-03-13 23:56:21.257][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-13 23:56:21.270][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:56:21.272][biodb::testThat]
biodb.TRACE[2025-03-13 23:56:21.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:21.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:21.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.395][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:21.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:21.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.413][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:21.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:21.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.433][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:21.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:21.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:21.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:21.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:21.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:21.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.491][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-13 23:56:21.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-13 23:56:21.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.510][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-13 23:56:21.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-13 23:56:21.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.529][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-13 23:56:21.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-13 23:56:21.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.548][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-13 23:56:21.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-13 23:56:21.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:21.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:21.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.699][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:21.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:21.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.718][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:21.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:21.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.738][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:21.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:21.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.758][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:21.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:21.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.778][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:21.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:21.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.798][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-13 23:56:21.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-13 23:56:21.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.818][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-13 23:56:21.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-13 23:56:21.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.838][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-13 23:56:21.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-13 23:56:21.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:21.851][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-13 23:56:21.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-13 23:56:21.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:21.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-13 23:56:21.907][biodb::testThat]
biodb.INFO [2025-03-13 23:56:21.910][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-13 23:56:21.913][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:56:21.926][biodb::testThat]
biodb.INFO [2025-03-13 23:56:21.967][biodb::testThat]
biodb.INFO [2025-03-13 23:56:21.970][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-13 23:56:21.982][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:56:21.985][biodb::testThat]
biodb.INFO [2025-03-13 23:56:22.024][biodb::testThat]
biodb.INFO [2025-03-13 23:56:22.026][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-13 23:56:22.038][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:56:22.041][biodb::testThat]
biodb.DEBUG[2025-03-13 23:56:22.061][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-03-13 23:56:22.763][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-03-13 23:56:23.669][biodb::testThat]
biodb.INFO [2025-03-13 23:56:23.685][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-13 23:56:23.688][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:56:23.690][biodb::testThat]
biodb.DEBUG[2025-03-13 23:56:24.148][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[2025-03-13 23:56:24.622][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:24.625][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:24.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:24.629][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:24.631][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:24.634][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:24.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:24.638][ef$get] fields variable is a list.
biodb.INFO [2025-03-13 23:56:24.642][biodb::testThat]
biodb.INFO [2025-03-13 23:56:24.644][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-03-13 23:56:24.646][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:56:24.648][biodb::testThat]
biodb.TRACE[2025-03-13 23:56:24.673][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:24.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:24.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:24.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:24.683][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:24.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:24.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:24.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:24.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:24.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:24.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:24.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:25.020][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:56:25.035][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:56:25.039][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-13 23:56:25.042][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:56:25.054][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-13 23:56:25.365][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:56:25.380][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:56:25.391][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-13 23:56:25.395][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:56:25.398][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-03-13 23:56:25.470][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 23:56:25.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 23:56:25.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:25.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:25.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:25.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:25.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:25.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:25.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:25.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:25.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:25.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:25.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:25.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:25.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:25.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:25.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:25.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:25.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:25.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:25.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:25.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:25.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:25.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:25.624][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:56:25.701][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:56:25.704][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:56:25.809][private$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[2025-03-13 23:56:26.225][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[2025-03-13 23:56:26.629][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:56:26.634][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-03-13 23:56:26.643][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-03-13 23:56:26.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:26.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:26.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:26.703][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:26.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:26.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:26.709][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[2025-03-13 23:56:26.711][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-03-13 23:56:26.864][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:56:26.867][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-03-13 23:56:26.870][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:56:26.883][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:56:26.886][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:56:26.888][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:56:26.890][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:56:26.903][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:56:26.909][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:26.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:26.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:26.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:26.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:26.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:26.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:27.033][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-03-13 23:56:27.040][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:56:27.050][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:56:27.053][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-03-13 23:56:32.517][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-03-13 23:56:32.946][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:56:32.951][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-03-13 23:56:32.959][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-03-13 23:56:32.965][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-03-13 23:56:32.969][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:56:32.972][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:56:32.974][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:56:32.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:32.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:32.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:32.993][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:32.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:32.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:32.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:56:33.004][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:33.006][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:33.008][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.011][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:33.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:33.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.023][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:33.025][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:33.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.029][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.032][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:33.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:33.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.042][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:33.044][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:33.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.049][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.052][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:33.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:33.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.061][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:33.064][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:33.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.068][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.071][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:33.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:33.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.080][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:33.083][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:33.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.088][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.108][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:33.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:33.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.138][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:33.141][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:33.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.145][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.171][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:33.175][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:33.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.180][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.192][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:33.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:33.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.208][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:33.211][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:33.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.215][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:33.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:33.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.237][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:33.250][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:33.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.254][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.266][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:33.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:33.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.303][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:33.305][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:33.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.309][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.312][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:33.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:33.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.332][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:33.345][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:33.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.349][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.352][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:33.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:33.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:33.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:33.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:33.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:33.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:33.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:33.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:33.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:33.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:33.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:33.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:33.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:33.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:33.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:33.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:33.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:33.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:33.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:33.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:33.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:33.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:33.629][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-03-13 23:56:33.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:33.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:33.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:33.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:33.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:33.717][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:33.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:33.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:33.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:33.738][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[2025-03-13 23:56:33.754][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:56:33.756][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:56:33.805][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-13 23:56:34.238][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-13 23:56:34.650][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:56:34.655][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-03-13 23:56:34.664][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-03-13 23:56:34.706][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:34.708][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:34.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:34.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:34.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:34.725][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:34.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:56:34.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:34.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:34.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:34.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:34.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:34.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:34.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:34.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:34.748][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:34.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:34.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:34.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:34.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:34.759][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:34.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:34.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:34.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:34.792][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:34.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:34.809][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-03-13 23:56:34.811][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:56:34.815][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-03-13 23:56:34.825][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:56:34.828][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:56:34.830][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:56:34.843][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:56:34.846][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:56:34.848][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:56:34.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:34.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:34.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:34.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:34.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:34.978][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:34.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:34.983][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-03-13 23:56:35.001][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:56:35.003][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:56:35.014][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-03-13 23:56:35.442][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-03-13 23:56:35.851][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:56:35.856][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-03-13 23:56:35.865][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-03-13 23:56:35.873][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-03-13 23:56:35.877][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:56:35.880][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:56:35.883][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:56:35.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:35.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:35.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:35.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:35.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:35.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:35.912][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[2025-03-13 23:56:35.918][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:35.920][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:35.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:35.925][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:35.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:35.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:35.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:35.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:35.938][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:35.940][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:35.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:35.944][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:35.947][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:35.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:35.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:35.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:35.958][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:36.077][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:36.085][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.118][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.122][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:36.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:36.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.134][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:36.138][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:36.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.166][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.170][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:36.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:36.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.198][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:36.201][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:36.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.242][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.249][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:36.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:36.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.302][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:36.305][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:36.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.309][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.330][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:36.338][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:36.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.343][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.346][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:36.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:36.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.427][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:36.438][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:36.440][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.443][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:36.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:36.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.479][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:36.482][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:36.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.501][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:36.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:36.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.529][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:36.549][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:36.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.554][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.557][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:36.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:36.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.593][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:36.596][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:36.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.602][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.616][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:36.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:36.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.645][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:36.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:36.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:36.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:36.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:36.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:36.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:36.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:36.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:36.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:36.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:36.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:36.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:36.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:36.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:36.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:36.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:36.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:36.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:37.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:37.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:37.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:37.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:37.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:37.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:37.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:37.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:37.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:37.132][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-03-13 23:56:37.135][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:37.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:37.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:37.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:37.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:37.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:37.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:37.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:37.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:37.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:37.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:37.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:37.367][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:56:37.396][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:56:37.410][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-13 23:56:37.413][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:56:37.416][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-13 23:56:37.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:37.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:37.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:37.466][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:37.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:37.482][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:37.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:56:37.487][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:37.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:37.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:37.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:37.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:37.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:37.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:37.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:37.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:37.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:37.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:37.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:37.550][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:37.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:37.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:37.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:37.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:37.596][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:37.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:37.617][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-03-13 23:56:37.621][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:56:37.633][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-03-13 23:56:37.636][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:56:37.639][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:56:37.642][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:56:37.655][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:56:37.658][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:56:37.660][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:56:37.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:37.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:37.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:37.713][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:37.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:37.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:37.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:37.732][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-03-13 23:56:37.749][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:56:37.752][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:56:37.765][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-03-13 23:56:38.175][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-03-13 23:56:38.588][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:56:38.592][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-03-13 23:56:38.600][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-03-13 23:56:38.606][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-03-13 23:56:38.610][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:56:38.612][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:56:38.615][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:56:38.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:38.621][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:38.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:38.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:38.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:38.639][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:38.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:56:38.646][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:38.648][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:38.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.652][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:38.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:38.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.664][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:38.667][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:38.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.671][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.674][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:38.676][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:38.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.680][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.683][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:38.686][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:38.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.690][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.693][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:38.696][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:38.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.700][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.702][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:38.705][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:38.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.709][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.712][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:38.715][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:38.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.719][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.721][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:38.724][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:38.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.729][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.731][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:38.756][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:38.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.771][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:38.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:38.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.792][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:38.795][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:38.804][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.806][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.809][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:38.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:38.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.828][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:38.831][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:38.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.844][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:38.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:38.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:38.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:38.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:38.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:38.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:38.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:38.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:38.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:38.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:38.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:38.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:38.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:38.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:38.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:38.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:38.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:38.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:39.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:39.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:39.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:39.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:39.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:39.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:39.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:39.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:39.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:39.053][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-03-13 23:56:39.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:39.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:39.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:39.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:39.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:39.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:39.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:39.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:39.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:39.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:39.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:39.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:39.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:39.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:39.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:39.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:39.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:39.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:39.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:39.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:39.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:39.152][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:39.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:39.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:39.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:39.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:39.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:39.208][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-03-13 23:56:39.211][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:56:39.223][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-03-13 23:56:39.227][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:56:39.230][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:56:39.241][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:56:39.244][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:56:39.246][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:56:39.248][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:56:39.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:39.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:39.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:39.290][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:39.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:39.306][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:39.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:39.311][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-03-13 23:56:39.325][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:56:39.327][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:56:39.339][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-03-13 23:56:39.753][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-03-13 23:56:40.215][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:56:40.220][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-03-13 23:56:40.228][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-03-13 23:56:40.235][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-03-13 23:56:40.238][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:56:40.241][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:56:40.244][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:56:40.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:40.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:40.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:40.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:40.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:40.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:40.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:56:40.274][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:40.276][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:40.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.280][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:40.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:40.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.293][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:40.295][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:40.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.299][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.302][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:40.305][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:40.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.309][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.312][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:40.314][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:40.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.318][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.321][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:40.324][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:40.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.328][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.331][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:40.334][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:40.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.338][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.341][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:40.343][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:40.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.348][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.351][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:40.353][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:40.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.366][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.374][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:40.377][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:40.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.382][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.386][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:40.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:40.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.400][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:40.404][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:40.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.419][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.422][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:40.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:40.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.441][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:40.444][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:40.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.459][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:40.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:40.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:40.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:40.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:40.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:40.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:40.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:40.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:40.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:40.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:40.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:40.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:40.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:40.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:40.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:40.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:40.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:40.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:40.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:40.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:40.642][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-03-13 23:56:40.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:40.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:40.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:40.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:40.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:40.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:40.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:40.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:40.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:40.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:40.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:40.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:40.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:40.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:40.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:40.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:40.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:40.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:40.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:40.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:40.794][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-03-13 23:56:40.807][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:56:40.811][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-03-13 23:56:40.824][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:56:40.826][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:56:40.829][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:56:40.831][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:56:40.833][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:56:40.844][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:56:40.850][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:40.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:40.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:40.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:40.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:40.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:40.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:40.900][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-03-13 23:56:40.916][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:56:40.919][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:56:40.922][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-03-13 23:56:41.346][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-03-13 23:56:41.750][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:56:41.755][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-03-13 23:56:41.764][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-03-13 23:56:41.771][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-03-13 23:56:41.776][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:56:41.779][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:56:41.782][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:56:41.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:41.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:41.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:41.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:41.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:41.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:41.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:56:41.817][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:41.820][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:41.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:41.825][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:41.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:41.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:41.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:41.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:41.840][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:41.843][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:41.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:41.848][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:41.852][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:41.855][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:41.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:41.860][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:41.863][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:41.866][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:41.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:41.872][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:41.875][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:41.878][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:41.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:41.883][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:41.886][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:41.889][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:41.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:41.894][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:41.898][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:41.901][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:41.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:41.906][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:41.909][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:41.930][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:41.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:41.944][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:41.947][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:41.950][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:41.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:41.963][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:41.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:41.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:41.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:41.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:41.998][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:42.001][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:42.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:42.007][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:42.047][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:42.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:42.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:42.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:42.058][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:42.060][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:42.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:42.066][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:42.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:42.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:42.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:42.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:42.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:42.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:42.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:42.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:42.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:42.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:42.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:42.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:42.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:42.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:42.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:42.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:42.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:42.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:42.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:42.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:42.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:42.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:42.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:42.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:42.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:42.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:42.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:42.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:42.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:42.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:42.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:42.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:42.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:42.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:42.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:42.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:42.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:42.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:42.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:42.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:42.330][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-03-13 23:56:42.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:42.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:42.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:42.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:42.350][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:42.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:42.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:42.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:42.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:42.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:42.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:42.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:42.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:42.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:42.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:42.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:42.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:42.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:42.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:42.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:42.435][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:42.437][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:42.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:42.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:42.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:42.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:42.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:42.493][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-03-13 23:56:42.496][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:56:42.500][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-03-13 23:56:42.515][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:56:42.517][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:56:42.520][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:56:42.522][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:56:42.536][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:56:42.538][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:56:42.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:42.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:42.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:42.582][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:42.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:42.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:42.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:42.598][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-03-13 23:56:42.612][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:56:42.616][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:56:42.619][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-03-13 23:56:43.046][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-03-13 23:56:43.482][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:56:43.486][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-03-13 23:56:43.495][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-03-13 23:56:43.501][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-03-13 23:56:43.505][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:56:43.508][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:56:43.510][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:56:43.513][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:43.515][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:43.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:43.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:43.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:43.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:43.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:56:43.540][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:43.542][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:43.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.546][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:43.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:43.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.558][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:43.561][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:43.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.565][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.568][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:43.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:43.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.577][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:43.579][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:43.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.584][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.587][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:43.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:43.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.596][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:43.599][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:43.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.603][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:43.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:43.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.628][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:43.630][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:43.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.635][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.637][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:43.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:43.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.646][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:43.649][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:43.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.653][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.666][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:43.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:43.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.685][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:43.688][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:43.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.703][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.707][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:43.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:43.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.726][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:43.729][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:43.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.742][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:43.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:43.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.768][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:43.770][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:43.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.774][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:43.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:43.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.816][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:43.818][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:43.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.832][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.835][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:43.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:43.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.857][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:43.859][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:43.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.874][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.877][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:43.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:43.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:43.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:43.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:43.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:43.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:43.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:43.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:43.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:43.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:43.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:43.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:43.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:43.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:43.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:43.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:44.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:44.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:44.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:44.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:44.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:44.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:44.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:44.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:44.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:44.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:44.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:44.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:44.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:44.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:44.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:44.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:44.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:44.099][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-03-13 23:56:44.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:44.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:44.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:44.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:44.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:44.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:44.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:44.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:44.138][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:44.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:44.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:44.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:44.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:44.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:44.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:44.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:44.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:44.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:44.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:44.208][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-03-13 23:56:44.211][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:56:44.214][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-03-13 23:56:44.227][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:56:44.230][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:56:44.232][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:56:44.234][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:56:44.245][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:56:44.247][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:56:44.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:44.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:44.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:44.290][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:44.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:44.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:44.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:44.311][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-03-13 23:56:44.328][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:56:44.330][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:56:44.334][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-03-13 23:56:44.766][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-03-13 23:56:45.181][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:56:45.185][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-03-13 23:56:45.193][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-03-13 23:56:45.199][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-03-13 23:56:45.203][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:56:45.205][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:56:45.208][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:56:45.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:45.213][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:45.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:45.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:45.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:45.230][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:45.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:56:45.237][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:45.239][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:45.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.257][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:45.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:45.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.269][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:45.271][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:45.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.276][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.278][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:45.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:45.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.287][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:45.290][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:45.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.294][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.298][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:45.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:45.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.307][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:45.309][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:45.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.314][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.316][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:45.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:45.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.326][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:45.330][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:45.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.335][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.337][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:45.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:45.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.357][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:45.373][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:45.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.377][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.380][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:45.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:45.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.403][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:45.417][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:45.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.422][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.425][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:45.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:45.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.446][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:45.449][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:45.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.453][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:45.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:45.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.474][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:45.494][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:45.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.498][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.502][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:45.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:45.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.519][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:45.521][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:45.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.535][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.538][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:45.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:45.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.558][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:45.561][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:45.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.565][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.568][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:45.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:45.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:45.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:45.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:45.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:45.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:45.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:45.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:45.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:45.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:45.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:45.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:45.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:45.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:45.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:45.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:45.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:45.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:45.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:45.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:45.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:45.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:45.826][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-03-13 23:56:45.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:45.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:45.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:45.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:45.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:45.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:45.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:45.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:45.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:45.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:45.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:45.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:45.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:45.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:45.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:45.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:45.951][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-03-13 23:56:45.963][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:56:45.967][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-03-13 23:56:45.971][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:56:45.984][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:56:45.986][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:56:45.989][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:56:45.992][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:56:46.005][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:56:46.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:46.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:46.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:46.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:46.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:46.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:46.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:46.114][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-03-13 23:56:46.196][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:56:46.199][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:56:46.218][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-03-13 23:56:46.687][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-03-13 23:56:47.111][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:56:47.116][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-03-13 23:56:47.124][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-03-13 23:56:47.130][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-03-13 23:56:47.133][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:56:47.136][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:56:47.138][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:56:47.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:47.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:47.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:47.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:47.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:47.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:47.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:56:47.168][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:47.171][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:47.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.175][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:47.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:47.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.187][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:47.190][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:47.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.194][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.197][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:47.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:47.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.206][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:47.208][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:47.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.212][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.215][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:47.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:47.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.224][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:47.227][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:47.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.231][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.234][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:47.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:47.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.243][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:47.245][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:47.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.250][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.252][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:47.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:47.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.270][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:47.273][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:47.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.283][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.286][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:47.289][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:47.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.301][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.304][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:47.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:47.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.320][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:47.322][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:47.325][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.327][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:47.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:47.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.360][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:47.384][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:47.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.394][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.397][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:47.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:47.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.418][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:47.420][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:47.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.435][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.437][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:47.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:47.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.457][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:47.460][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:47.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.474][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.477][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:47.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:47.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:47.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:47.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:47.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:47.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:47.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:47.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:47.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:47.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:47.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:47.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:47.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:47.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:47.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:47.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:47.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:47.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:47.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:47.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:47.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:47.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:47.682][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-03-13 23:56:47.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:47.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:47.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:47.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:47.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:47.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:47.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:47.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:47.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:47.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:47.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:47.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:47.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:47.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:47.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:47.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:47.791][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-03-13 23:56:48.164][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:56:48.168][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-03-13 23:56:48.171][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:56:48.183][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:56:48.186][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:56:48.189][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:56:48.191][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:56:48.202][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:56:48.208][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:48.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:48.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:48.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:48.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:48.248][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:48.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:48.263][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-03-13 23:56:48.269][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:56:48.285][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:56:48.288][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-03-13 23:56:48.727][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-03-13 23:56:49.134][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:56:49.138][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-03-13 23:56:49.146][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-03-13 23:56:49.151][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-03-13 23:56:49.155][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:56:49.158][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:56:49.160][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:56:49.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:49.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:49.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:49.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:49.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:49.182][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:49.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:56:49.189][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:49.191][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:49.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.221][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:49.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:49.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.233][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:49.235][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:49.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.240][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.243][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:49.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:49.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.276][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:49.278][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:49.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.283][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.286][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:49.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:49.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.294][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:49.297][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:49.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.301][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.304][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:49.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:49.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.313][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:49.315][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:49.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.322][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.325][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:49.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:49.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.340][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:49.343][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:49.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.355][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.358][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:49.361][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:49.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.365][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.367][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:49.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:49.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.377][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:49.380][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:49.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.385][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:49.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:49.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.411][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:49.414][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:49.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.420][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.436][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:49.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:49.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.458][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:49.461][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:49.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.475][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.479][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:49.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:49.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.511][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:49.514][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:49.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.520][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.533][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:49.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:49.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:49.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:49.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:49.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:49.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:49.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:49.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:49.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:49.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:49.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:49.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:49.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:49.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:49.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:49.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:49.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:49.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:49.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:49.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:49.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:49.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:49.820][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-03-13 23:56:49.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:49.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:49.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:49.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:49.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:49.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:49.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:49.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:49.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:49.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:49.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:49.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:49.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:49.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:49.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:49.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:49.936][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-03-13 23:56:49.960][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:56:49.965][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-03-13 23:56:49.982][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:56:49.986][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:56:49.990][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:56:50.001][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:56:50.004][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:56:50.007][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:56:50.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:50.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:50.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:50.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:50.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:50.101][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:50.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:50.107][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-03-13 23:56:50.117][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:56:50.161][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:56:50.165][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-03-13 23:56:50.590][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-03-13 23:56:51.007][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:56:51.013][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-03-13 23:56:51.022][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-03-13 23:56:51.031][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-03-13 23:56:51.036][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:56:51.039][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:56:51.043][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:56:51.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:51.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:51.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:51.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:51.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:51.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:51.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:56:51.082][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:51.085][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:51.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.091][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:51.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:51.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.108][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:51.111][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:51.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.117][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.121][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:51.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:51.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.134][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:51.137][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:51.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.143][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.147][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:51.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:51.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.167][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:51.170][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:51.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.182][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.187][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:51.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:51.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.211][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:51.226][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:51.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.232][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:51.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:51.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.272][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:51.284][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:51.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.291][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.305][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:51.308][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:51.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.328][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.333][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:51.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:51.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.369][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:51.373][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:51.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.389][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:51.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:51.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.432][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:51.436][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:51.449][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.454][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.459][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:51.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:51.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.493][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:51.497][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:51.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.509][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.513][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:51.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:51.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.581][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:51.585][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:51.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.600][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.605][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:51.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:51.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:51.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:51.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:51.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:51.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:51.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:51.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:51.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:51.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:51.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:51.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:51.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:51.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:51.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:51.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:51.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:51.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:51.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:51.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:51.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:51.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:51.898][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-03-13 23:56:51.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:51.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:51.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:51.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:51.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:51.940][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:51.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:51.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:51.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:51.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:51.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:51.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:51.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:52.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:52.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:52.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:52.020][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-03-13 23:56:52.024][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:56:52.027][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-03-13 23:56:52.042][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:56:52.044][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:56:52.047][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:56:52.063][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:56:52.071][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:56:52.073][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:56:52.092][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:52.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:52.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:52.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:52.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:52.128][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:52.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:52.143][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-03-13 23:56:52.159][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:56:52.162][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:56:52.165][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-03-13 23:56:52.591][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-03-13 23:56:52.996][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:56:53.000][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-03-13 23:56:53.008][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-03-13 23:56:53.014][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-03-13 23:56:53.018][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:56:53.020][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:56:53.023][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:56:53.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:53.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:53.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:53.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:53.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:53.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:53.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:56:53.052][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:53.055][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:53.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.059][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:53.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:53.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.071][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:53.073][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:53.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.077][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.080][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:53.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:53.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.089][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:53.092][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:53.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.097][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.100][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:53.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:53.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.109][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:53.111][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:53.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.116][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.118][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:53.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:53.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.128][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:53.130][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:53.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.142][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.145][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:53.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:53.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.159][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:53.161][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:53.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.175][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.178][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:53.181][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:53.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.194][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.197][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:53.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:53.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.211][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:53.214][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:53.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.230][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:53.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:53.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.258][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:53.261][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:53.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.277][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.280][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:53.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:53.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.300][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:53.303][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:53.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.315][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.318][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:53.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:53.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.337][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:53.340][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:53.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.361][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.364][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:53.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:53.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:53.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:53.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:53.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:53.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:53.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:53.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:53.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:53.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:53.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:53.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:53.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:53.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:53.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:53.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:53.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:53.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:53.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:53.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:53.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:53.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:53.600][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-03-13 23:56:53.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:53.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:53.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.632][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:53.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:53.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:53.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:53.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:53.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:53.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:53.681][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:53.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:53.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:53.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:53.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:53.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:53.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:53.724][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-03-13 23:56:53.735][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:56:53.739][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-03-13 23:56:53.741][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:56:53.753][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:56:53.757][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:56:53.760][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:56:53.763][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:56:53.773][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:56:53.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:53.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:53.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:53.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:53.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:53.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:53.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:53.828][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-03-13 23:56:53.846][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:56:53.849][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:56:53.852][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-03-13 23:56:54.302][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-03-13 23:56:54.712][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:56:54.717][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-03-13 23:56:54.725][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-03-13 23:56:54.731][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-03-13 23:56:54.735][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:56:54.738][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:56:54.741][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:56:54.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:54.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:54.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:54.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:54.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:54.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:54.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:56:54.772][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:54.774][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:54.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:54.779][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:54.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:54.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:54.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:54.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:54.791][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:54.793][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:54.796][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:54.798][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:54.801][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:54.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:54.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:54.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:54.811][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:54.813][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:54.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:54.818][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:54.821][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:54.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:54.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:54.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:54.831][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:54.833][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:54.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:54.838][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:54.845][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:54.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:54.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:54.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:54.862][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:54.864][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:54.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:54.869][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:54.877][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:54.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:54.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:54.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:54.894][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:54.896][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:54.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:54.938][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:54.951][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:54.954][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:54.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:54.958][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:54.976][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:54.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:54.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:54.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:54.992][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:54.994][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:54.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:54.999][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:55.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:55.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.020][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:55.032][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:55.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.037][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.051][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:55.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:55.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.071][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:55.074][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:55.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.078][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.093][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:55.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:55.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.114][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:55.116][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:55.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.121][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.135][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:55.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:55.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:55.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:55.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:55.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:55.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:55.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:55.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:55.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:55.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:55.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:55.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:55.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:55.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:55.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:55.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:55.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:55.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:55.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:55.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:55.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:55.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:55.388][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-03-13 23:56:55.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:55.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:55.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:55.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:55.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:55.413][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:55.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:55.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:55.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:55.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:55.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:55.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:55.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:55.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:55.470][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:55.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:55.476][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-03-13 23:56:55.478][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:56:55.492][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-03-13 23:56:55.495][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:56:55.503][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:56:55.507][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:56:55.509][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:56:55.512][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:56:55.525][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:56:55.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:55.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:55.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:55.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:55.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:55.583][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:55.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:55.588][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-03-13 23:56:55.606][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:56:55.609][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:56:55.623][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-03-13 23:56:56.043][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-03-13 23:56:56.452][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:56:56.458][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-03-13 23:56:56.467][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-03-13 23:56:56.475][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-03-13 23:56:56.480][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:56:56.484][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:56:56.488][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:56:56.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:56.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:56.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:56.511][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:56.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:56.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:56.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:56:56.527][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:56.544][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:56.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:56.550][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:56.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:56.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:56.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:56.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:56.587][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:56.591][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:56.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:56.597][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:56.600][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:56.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:56.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:56.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:56.642][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:56.646][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:56.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:56.651][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:56.666][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:56.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:56.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:56.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:56.691][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:56.705][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:56.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:56.710][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:56.725][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:56.729][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:56.733][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:56.735][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:56.750][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:56.753][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:56.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:56.770][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:56.775][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:56.778][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:56.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:56.795][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:56.799][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:56.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:56.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:56.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:56.818][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:56.832][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:56.834][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:56.837][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:56.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:56.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:56.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:56.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:56.875][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:56.878][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:56.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:56.884][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:56.895][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:56.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:56.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:56.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:56.917][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:56.919][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:56.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:56.924][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:56.940][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:56.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:56.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:56.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:56.964][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:56.966][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:56.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:56.982][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:56.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:56.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:56.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:57.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:57.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:57.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:57.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:57.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:57.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:57.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:57.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:57.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:57.048][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:57.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:57.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:57.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:57.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:57.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:57.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:57.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:57.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:57.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:57.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:57.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:57.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:57.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:57.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:57.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:57.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:57.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:57.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:57.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:57.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:57.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:57.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:57.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:57.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:57.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:57.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:57.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:57.193][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-03-13 23:56:57.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:57.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:57.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:57.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:57.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:57.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:57.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:57.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:57.236][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:57.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:57.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:57.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:57.256][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:57.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:57.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:57.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:57.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:57.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:57.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:57.304][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-03-13 23:56:57.317][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:56:57.321][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-03-13 23:56:57.324][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:56:57.328][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:56:57.342][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:56:57.345][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:56:57.347][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:56:57.349][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:56:57.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:57.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:57.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:57.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:57.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:57.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:57.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:57.423][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-03-13 23:56:57.429][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:56:57.443][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:56:57.446][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-03-13 23:56:57.879][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-03-13 23:56:58.278][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:56:58.283][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-03-13 23:56:58.291][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-03-13 23:56:58.298][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-03-13 23:56:58.301][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:56:58.304][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:56:58.307][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:56:58.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:58.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:58.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:58.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:58.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:58.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:58.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:56:58.337][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:58.357][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:58.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.362][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:58.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:58.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.373][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:58.376][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:58.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.380][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.382][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:56:58.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:56:58.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.392][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:58.395][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:58.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.399][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.401][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:56:58.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:56:58.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.411][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:56:58.414][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:56:58.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.418][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.420][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:56:58.422][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:56:58.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.426][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.429][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:58.432][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:56:58.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.437][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.439][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:58.442][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:58.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.446][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.460][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:56:58.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:58.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.480][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:58.483][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:58.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.487][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:58.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:56:58.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.520][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:58.523][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:58.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.534][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.538][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:56:58.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:56:58.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.560][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:58.562][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:58.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.575][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.579][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:56:58.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:56:58.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.597][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:56:58.600][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:56:58.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.613][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:58.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:58.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:58.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:58.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:58.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:58.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:56:58.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:56:58.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:58.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:58.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:58.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:58.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:58.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:58.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:58.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:58.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:58.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:58.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:56:58.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:56:58.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:58.806][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-03-13 23:56:58.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:58.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:58.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:58.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:58.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:56:58.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:58.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:56:58.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:56:58.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:56:58.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:58.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:58.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:58.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:58.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:58.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:58.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:58.920][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-03-13 23:56:58.922][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:56:58.926][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-03-13 23:56:58.965][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:56:58.969][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:56:58.972][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:56:58.984][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:56:58.987][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:56:58.989][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:56:59.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:59.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:59.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:56:59.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:56:59.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:56:59.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:56:59.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:56:59.049][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-03-13 23:56:59.086][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:56:59.092][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:56:59.098][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-03-13 23:56:59.552][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-03-13 23:56:59.958][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:56:59.963][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-03-13 23:56:59.971][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-03-13 23:56:59.977][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-03-13 23:56:59.981][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:56:59.984][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:56:59.986][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:56:59.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:56:59.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:56:59.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:00.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:00.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:00.009][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:00.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:00.016][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:00.018][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:00.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.023][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:00.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:00.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.034][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:00.037][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:00.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.041][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.044][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:00.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:00.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.053][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:00.055][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:00.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.059][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.062][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:00.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:00.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.071][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:00.073][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:00.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.078][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.080][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:00.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:00.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.089][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:00.092][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:00.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.097][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.100][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:00.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:00.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.118][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:00.121][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:00.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.126][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.129][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:00.132][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:00.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.146][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.149][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:00.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:00.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.169][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:00.172][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:00.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.186][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:00.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:00.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.209][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:00.211][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:00.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.223][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.226][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:00.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:00.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.245][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:00.247][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:00.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.261][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.264][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:00.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:00.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.280][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:00.283][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:00.285][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.297][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.300][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:00.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:00.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:00.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:00.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:00.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:00.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:00.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:00.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:00.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:00.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:00.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:00.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:00.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:00.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:00.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:00.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:00.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:00.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:00.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:00.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:00.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:00.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:00.520][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-03-13 23:57:00.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:00.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:00.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:00.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:00.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:00.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:00.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:00.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:00.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:00.590][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:00.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:00.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:00.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:00.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:00.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:00.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:00.654][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-03-13 23:57:00.657][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:57:00.660][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-03-13 23:57:00.673][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:57:00.676][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:57:00.678][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:57:00.681][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:57:00.694][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:57:00.696][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:57:00.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:00.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:00.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:00.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:00.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:00.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:00.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:00.787][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-03-13 23:57:00.804][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:00.806][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:00.809][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-03-13 23:57:01.248][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-03-13 23:57:01.670][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:01.674][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-03-13 23:57:01.736][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-03-13 23:57:01.743][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-03-13 23:57:01.746][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:57:01.749][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:57:01.752][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:57:01.755][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:01.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:01.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:01.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:01.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:01.775][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:01.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:01.782][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:01.784][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:01.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:01.788][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:01.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:01.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:01.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:01.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:01.801][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:01.803][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:01.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:01.808][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:01.811][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:01.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:01.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:01.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:01.820][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:01.823][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:01.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:01.827][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:01.830][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:01.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:01.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:01.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:01.839][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:01.842][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:01.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:01.847][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:01.850][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:01.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:01.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:01.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:01.860][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:01.863][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:01.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:01.869][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:01.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:01.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:01.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:01.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:01.890][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:01.892][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:01.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:01.905][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:01.908][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:01.910][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:01.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:01.924][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:01.927][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:01.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:01.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:01.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:01.947][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:01.950][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:01.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:01.965][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:01.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:01.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:01.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:01.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:01.989][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:01.991][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:01.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.006][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:02.009][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:02.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:02.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:02.028][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:02.031][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:02.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.046][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:02.049][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:02.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:02.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:02.070][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:02.072][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:02.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.088][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:02.091][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:02.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:02.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:02.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:02.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:02.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:02.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:02.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:02.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:02.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:02.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:02.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:02.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:02.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:02.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:02.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:02.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:02.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:02.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:02.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:02.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:02.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:02.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:02.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:02.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:02.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:02.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:02.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:02.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:02.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:02.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:02.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:02.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:02.277][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-03-13 23:57:02.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:02.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:02.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:02.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:02.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:02.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:02.309][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:02.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:02.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:02.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:02.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:02.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:02.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:02.349][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:02.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:02.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:02.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:02.358][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-03-13 23:57:02.363][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:57:02.367][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-03-13 23:57:02.370][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:57:02.375][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:57:02.378][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:57:02.380][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:57:02.383][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:57:02.387][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:57:02.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:02.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:02.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:02.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:02.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:02.416][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:02.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:02.421][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-03-13 23:57:02.427][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:02.430][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:02.433][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-03-13 23:57:02.859][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-03-13 23:57:03.275][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:03.280][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-03-13 23:57:03.288][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-03-13 23:57:03.293][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-03-13 23:57:03.297][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:57:03.300][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:57:03.302][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:57:03.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:03.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:03.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:03.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:03.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:03.326][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:03.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:03.333][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:03.335][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:03.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.340][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:03.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:03.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.352][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:03.354][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:03.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.358][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.360][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:03.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:03.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.369][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:03.371][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:03.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.375][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.378][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:03.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:03.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.387][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:03.390][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:03.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.394][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.396][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:03.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:03.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.405][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:03.408][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:03.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.420][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.423][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:03.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:03.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.443][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:03.446][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:03.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.461][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.465][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:03.468][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:03.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.474][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.478][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:03.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:03.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.488][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:03.490][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:03.493][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.495][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:03.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:03.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.533][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:03.545][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:03.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.554][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.566][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:03.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:03.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.597][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:03.608][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:03.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.613][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.621][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:03.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:03.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.631][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:03.648][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:03.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.653][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.655][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:03.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:03.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:03.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:03.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:03.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:03.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:03.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:03.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:03.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:03.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:03.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:03.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:03.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:03.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:03.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:03.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:03.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:03.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:03.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:03.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:03.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:03.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:03.942][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-03-13 23:57:03.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:03.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:03.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:03.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:03.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:03.992][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:03.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:03.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:03.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:04.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:04.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:04.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:04.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:04.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:04.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:04.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:04.058][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-03-13 23:57:04.061][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:57:04.075][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-03-13 23:57:04.078][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:57:04.080][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:57:04.091][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:57:04.093][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:57:04.095][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:57:04.098][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:57:04.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:04.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:04.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:04.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:04.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:04.155][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:04.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:04.160][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-03-13 23:57:04.175][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:04.177][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:04.181][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-03-13 23:57:04.599][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-03-13 23:57:05.221][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:05.226][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-03-13 23:57:05.235][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-03-13 23:57:05.242][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-03-13 23:57:05.247][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:57:05.250][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:57:05.253][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:57:05.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:05.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:05.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:05.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:05.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:05.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:05.282][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.TRACE[2025-03-13 23:57:05.288][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:05.290][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:05.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.295][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:05.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:05.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.308][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:05.310][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:05.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.315][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.317][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:05.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:05.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.327][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:05.330][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:05.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.334][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.337][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:05.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:05.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.347][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:05.349][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:05.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.354][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.357][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:05.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:05.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.366][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:05.369][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:05.372][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.374][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.379][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:05.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:05.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.390][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:05.393][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:05.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.409][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.413][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:05.424][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:05.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.430][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.443][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:05.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:05.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.466][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:05.469][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:05.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.484][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:05.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:05.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.509][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:05.523][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:05.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.530][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:05.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:05.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.567][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:05.569][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:05.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.583][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.586][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:05.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:05.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.605][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:05.608][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:05.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.623][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.626][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:05.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:05.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:05.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:05.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:05.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:05.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:05.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:05.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:05.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:05.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:05.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:05.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:05.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:05.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:05.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:05.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:05.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:05.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:05.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:05.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:05.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:05.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:05.834][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-03-13 23:57:05.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:05.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:05.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:05.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:05.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:05.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:05.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:05.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:05.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:05.884][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:05.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:05.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:05.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:05.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:05.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:05.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:05.943][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-03-13 23:57:05.945][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:57:05.967][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-03-13 23:57:05.971][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:57:05.973][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:57:05.984][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:57:05.987][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:57:05.989][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:57:05.991][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:57:06.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:06.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:06.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:06.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:06.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:06.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:06.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:06.055][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-03-13 23:57:06.072][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:06.074][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:06.088][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-03-13 23:57:06.499][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-03-13 23:57:06.911][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:06.915][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-03-13 23:57:06.923][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-03-13 23:57:06.930][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-03-13 23:57:06.966][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:57:06.969][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:57:06.972][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:57:06.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:06.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:06.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:06.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:06.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:06.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:06.997][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[2025-03-13 23:57:07.002][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:07.004][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:07.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.009][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:07.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:07.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.021][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:07.024][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:07.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.028][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.031][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:07.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:07.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.042][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:07.044][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:07.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.048][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.052][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:07.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:07.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.062][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:07.064][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:07.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.068][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.071][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:07.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:07.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.082][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:07.084][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:07.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.089][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:07.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:07.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.103][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:07.105][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:07.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.118][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.120][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:07.124][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:07.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.140][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.143][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:07.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:07.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.211][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:07.213][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:07.215][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.228][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:07.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:07.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.253][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:07.256][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:07.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.271][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.274][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:07.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:07.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.297][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:07.300][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:07.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.316][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.319][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:07.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:07.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.341][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:07.343][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:07.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.359][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.363][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:07.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:07.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:07.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:07.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:07.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:07.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:07.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:07.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:07.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:07.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:07.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:07.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:07.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:07.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:07.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:07.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:07.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:07.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:07.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:07.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:07.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:07.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:07.580][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-03-13 23:57:07.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:07.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:07.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:07.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:07.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:07.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:07.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:07.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:07.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:07.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:07.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:07.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:07.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:07.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:07.680][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:07.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:07.686][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-03-13 23:57:07.700][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:57:07.704][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-03-13 23:57:07.707][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:57:07.720][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:57:07.723][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:57:07.726][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:57:07.728][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:57:07.741][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:57:07.748][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:07.760][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:07.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:07.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:07.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:07.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:07.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:07.803][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-03-13 23:57:07.810][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:07.822][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:07.825][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-03-13 23:57:08.247][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-03-13 23:57:08.660][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:08.664][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-03-13 23:57:08.695][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-03-13 23:57:08.702][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-03-13 23:57:08.706][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:57:08.708][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:57:08.711][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:57:08.715][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:08.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:08.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:08.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:08.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:08.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:08.736][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[2025-03-13 23:57:08.741][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:08.743][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:08.745][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:08.747][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:08.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:08.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:08.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:08.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:08.758][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:08.761][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:08.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:08.765][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:08.768][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:08.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:08.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:08.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:08.776][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:08.779][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:08.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:08.783][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:08.786][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:08.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:08.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:08.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:08.795][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:08.797][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:08.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:08.801][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:08.804][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:08.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:08.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:08.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:08.813][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:08.815][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:08.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:08.819][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:08.822][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:08.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:08.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:08.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:08.831][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:08.833][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:08.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:08.837][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:08.840][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:08.842][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:08.850][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:08.852][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:08.854][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:08.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:08.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:08.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:08.877][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:08.880][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:08.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:08.894][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:08.897][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:08.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:08.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:08.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:08.918][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:08.933][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:08.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:08.938][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:08.942][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:08.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:08.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:08.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:08.973][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:08.976][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:08.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:08.981][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:08.994][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:08.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:09.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:09.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:09.015][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:09.018][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:09.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:09.033][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:09.036][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:09.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:09.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:09.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:09.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:09.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:09.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:09.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:09.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:09.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:09.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:09.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:09.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:09.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:09.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:09.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:09.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:09.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:09.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:09.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:09.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:09.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:09.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:09.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:09.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:09.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:09.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:09.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:09.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:09.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:09.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:09.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:09.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:09.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:09.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:09.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:09.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:09.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:09.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:09.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:09.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:09.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:09.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:09.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:09.247][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-03-13 23:57:09.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:09.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:09.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:09.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:09.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:09.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:09.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:09.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:09.309][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:09.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:09.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:09.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:09.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:09.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:09.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:09.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:09.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:09.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:09.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:09.419][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-03-13 23:57:09.433][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:57:09.437][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-03-13 23:57:09.465][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:57:09.469][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:57:09.472][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:57:09.486][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:57:09.489][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:57:09.492][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:57:09.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:09.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:09.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:09.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:09.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:09.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:09.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:09.551][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-03-13 23:57:09.570][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:09.594][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:09.597][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-03-13 23:57:10.023][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-03-13 23:57:10.448][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:10.451][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-03-13 23:57:10.466][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-03-13 23:57:10.472][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-03-13 23:57:10.477][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:57:10.479][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:57:10.482][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:57:10.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:10.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:10.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:10.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:10.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:10.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:10.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:10.554][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:10.563][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:10.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.568][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:10.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:10.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.588][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:10.600][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:10.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.604][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.607][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:10.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:10.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.617][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:10.619][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:10.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.623][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.626][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:10.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:10.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.636][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:10.638][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:10.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.643][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.645][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:10.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:10.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.655][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:10.657][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:10.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.663][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.666][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:10.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:10.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.691][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:10.693][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:10.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.714][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.717][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:10.719][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:10.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.729][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.746][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:10.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:10.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.753][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:10.757][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:10.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.761][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:10.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:10.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.775][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:10.776][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:10.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.779][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:10.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:10.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.799][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:10.800][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:10.801][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.802][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.804][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:10.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:10.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.823][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:10.826][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:10.828][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.830][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.841][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:10.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:10.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:10.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:10.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:10.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:10.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:10.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:10.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:10.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:10.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:10.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:10.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:10.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:10.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:10.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:10.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:10.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:10.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:11.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:11.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:11.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:11.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:11.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:11.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:11.076][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-03-13 23:57:11.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.098][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:11.237][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:11.245][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:11.258][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-13 23:57:11.261][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:11.264][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-13 23:57:11.271][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:11.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:11.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:11.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:11.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:11.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:11.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:11.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:11.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:11.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:11.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:11.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:11.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:11.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:11.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:11.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:11.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:11.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:11.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:11.582][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:11.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:11.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:11.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:11.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:11.701][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:11.703][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:11.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:11.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:11.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:11.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:11.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:11.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.764][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:11.851][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:11.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:11.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:11.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:11.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:11.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:11.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:11.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:11.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:11.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:11.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:11.967][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:11.969][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:11.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:11.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:12.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:12.008][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:12.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:12.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:12.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:12.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:12.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:12.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:12.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:12.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:12.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:12.123][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:12.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:12.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:12.148][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:12.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:12.199][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:12.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:12.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:12.246][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:12.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:12.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:12.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:12.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:12.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:12.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:12.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:12.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:12.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:12.359][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:12.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:12.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:12.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:12.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:12.402][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:12.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:12.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:12.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:12.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:12.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:12.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:12.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:12.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:12.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:12.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:12.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:12.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:12.611][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:12.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:12.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:12.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:12.650][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:12.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:12.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:12.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:12.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:12.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:12.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:12.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:12.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:12.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:12.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:12.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:12.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:12.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:12.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:12.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:12.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:12.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:12.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:12.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:12.871][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:12.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:12.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:12.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:12.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:12.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:12.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:12.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:12.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:12.976][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:12.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:12.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:12.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:12.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:12.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.037][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:13.055][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:13.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:13.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:13.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:13.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:13.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:13.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:13.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:13.154][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:13.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:13.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:13.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:13.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:13.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:13.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:13.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.240][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:13.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:13.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:13.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:13.298][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:13.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:13.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:13.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:13.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.326][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:13.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:13.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:13.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:13.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:13.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:13.409][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:13.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:13.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:13.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:13.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:13.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:13.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:13.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:13.500][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:13.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:13.504][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:13.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:13.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:13.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:13.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:13.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:13.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:13.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:13.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.581][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:13.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:13.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:13.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:13.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:13.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:13.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:13.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:13.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:13.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:13.674][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:13.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:13.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:13.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:13.875][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:13.905][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:13.908][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:13.913][private$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[2025-03-13 23:57:14.350][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[2025-03-13 23:57:14.773][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:14.778][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-03-13 23:57:14.788][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-03-13 23:57:14.796][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[2025-03-13 23:57:14.804][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:14.806][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:14.811][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-13 23:57:15.227][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-13 23:57:15.636][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:15.643][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-03-13 23:57:15.710][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-03-13 23:57:15.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:15.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:15.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:15.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:15.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:15.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:15.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:15.741][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-03-13 23:57:15.743][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:57:15.747][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-03-13 23:57:15.750][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:57:15.752][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:57:15.756][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:57:15.758][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:57:15.760][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:57:15.763][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:57:15.768][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:15.770][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:15.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:15.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:15.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:15.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:15.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:15.793][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-03-13 23:57:15.799][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:15.801][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:15.804][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-03-13 23:57:16.227][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-03-13 23:57:16.662][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:16.666][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-03-13 23:57:16.673][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-03-13 23:57:16.677][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-03-13 23:57:16.680][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:57:16.681][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:57:16.687][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:57:16.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:16.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:16.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:16.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:16.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:16.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:16.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:16.719][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:16.721][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:16.722][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.726][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:16.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:16.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.733][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:16.735][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:16.736][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.738][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.740][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:16.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:16.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.746][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:16.747][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:16.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.750][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:16.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:16.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.763][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:16.764][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:16.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.768][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.771][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:16.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:16.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.780][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:16.782][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:16.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.786][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.788][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:16.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:16.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.797][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:16.804][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:16.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.806][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.808][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:16.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:16.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.815][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:16.817][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:16.819][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.821][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.824][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:16.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:16.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.834][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:16.835][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:16.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.839][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:16.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:16.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.853][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:16.855][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:16.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.860][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.863][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:16.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:16.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.873][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:16.875][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:16.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.880][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.892][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:16.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:16.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.897][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:16.899][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:16.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.903][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.904][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:16.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:16.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:16.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:16.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:16.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:16.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:16.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:16.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:16.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:16.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:16.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:16.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:16.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:16.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:16.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:16.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:16.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:16.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:16.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:16.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:16.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:16.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:16.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:17.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:17.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:17.003][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-03-13 23:57:17.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:17.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:17.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:17.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:17.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:17.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:17.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:17.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:17.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:17.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:17.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:17.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:17.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:17.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:17.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:17.038][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:17.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:17.042][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:17.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:17.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:17.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:17.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:17.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:17.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:17.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:17.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:17.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:17.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:17.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:17.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:17.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:17.060][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:17.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:17.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:17.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:17.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:17.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:17.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:17.075][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-03-13 23:57:17.077][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:57:17.079][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-03-13 23:57:17.081][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:57:17.082][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:57:17.085][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:57:17.088][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:57:17.089][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:57:17.091][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:57:17.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:17.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:17.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:17.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:17.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:17.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:17.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:17.113][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-03-13 23:57:17.127][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:17.129][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:17.132][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-03-13 23:57:17.732][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-03-13 23:57:18.142][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:18.144][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-03-13 23:57:18.161][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-03-13 23:57:18.165][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-03-13 23:57:18.169][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:57:18.170][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:57:18.172][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:57:18.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:18.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:18.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:18.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:18.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:18.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:18.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:18.192][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:18.195][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:18.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.212][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:18.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:18.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.221][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:18.223][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:18.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.225][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.227][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:18.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:18.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.238][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:18.241][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:18.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.270][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.271][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:18.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:18.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.277][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:18.287][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:18.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.291][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.293][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:18.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:18.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.298][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:18.299][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:18.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.307][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.309][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:18.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:18.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.317][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:18.318][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:18.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.322][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.324][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:18.325][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:18.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.327][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.329][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:18.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:18.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.334][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.336][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.338][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.354][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:18.355][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:18.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.358][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.359][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:18.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:18.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.365][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:18.367][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:18.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.369][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.371][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:18.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:18.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.378][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:18.379][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:18.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.382][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.383][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:18.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:18.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.388][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:18.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:18.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:18.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:18.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:18.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:18.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:18.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:18.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:18.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:18.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:18.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:18.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:18.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:18.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:18.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:18.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:18.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:18.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:18.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:18.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:18.445][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-03-13 23:57:18.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:18.489][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:18.493][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:18.495][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-13 23:57:18.497][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:18.499][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-13 23:57:18.505][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:18.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:18.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:18.514][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:18.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:18.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:18.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:18.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:18.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:18.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:18.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:18.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:18.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:18.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:18.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:18.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.593][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:18.603][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:18.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:18.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:18.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:18.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:18.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:18.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:18.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:18.687][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:18.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:18.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:18.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:18.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:18.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:18.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:18.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:18.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:18.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:18.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:18.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:18.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:18.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:18.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:18.754][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:18.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:18.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:18.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:18.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:18.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:18.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:18.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:18.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.793][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:18.803][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:18.804][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:18.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:18.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:18.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:18.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:18.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:18.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.858][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:18.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:18.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:18.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:18.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:18.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:18.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:18.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:18.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:18.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:18.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:18.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:18.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:18.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:18.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:18.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:18.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.940][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:18.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:18.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:18.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:18.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:18.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:18.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:18.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:18.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:18.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:18.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:18.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:18.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:18.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:18.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:18.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:18.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:18.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:18.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:18.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:19.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:19.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:19.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:19.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:19.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:19.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:19.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:19.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:19.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:19.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:19.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:19.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:19.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:19.064][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:19.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:19.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:19.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:19.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:19.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:19.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:19.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:19.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:19.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:19.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.131][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:19.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:19.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:19.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:19.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:19.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:19.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:19.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:19.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:19.179][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:19.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:19.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:19.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:19.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:19.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:19.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:19.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:19.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:19.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:19.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:19.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:19.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:19.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:19.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:19.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:19.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:19.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:19.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:19.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:19.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:19.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:19.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:19.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:19.288][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:19.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:19.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:19.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:19.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:19.300][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:19.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:19.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:19.342][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:19.344][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:19.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:19.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:19.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:19.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:19.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:19.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:19.408][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:19.415][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:19.418][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-13 23:57:19.420][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:19.423][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-13 23:57:19.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:19.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:19.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:19.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:19.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:19.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:19.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:19.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:19.527][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:19.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:19.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:19.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:19.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:19.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:19.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:19.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:19.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:19.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:19.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:19.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:19.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:19.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:19.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:19.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:19.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:19.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:19.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:19.757][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:19.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:19.760][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:19.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:19.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:19.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:19.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:19.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:19.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:19.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:19.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:19.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:19.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:19.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:19.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:19.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:19.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:19.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:19.854][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:19.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:19.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:19.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:19.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:19.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:19.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:19.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:19.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:19.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:19.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:19.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:19.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:19.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:19.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:19.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:19.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:19.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:19.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:19.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:19.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:19.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:19.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:19.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:19.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:20.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:20.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:20.007][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:20.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:20.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:20.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:20.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:20.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:20.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:20.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:20.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:20.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:20.057][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:20.088][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:20.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:20.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:20.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:20.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:20.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:20.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:20.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:20.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:20.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:20.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:20.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:20.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:20.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:20.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:20.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:20.208][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:20.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:20.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:20.220][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:20.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:20.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:20.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:20.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.243][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:20.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:20.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:20.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:20.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:20.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:20.277][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:20.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:20.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:20.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:20.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:20.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:20.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:20.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:20.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:20.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:20.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:20.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:20.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:20.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:20.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:20.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:20.359][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:20.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:20.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:20.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:20.398][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:20.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:20.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:20.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:20.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:20.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:20.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:20.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:20.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:20.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:20.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:20.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:20.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:20.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:20.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:20.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:20.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:20.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:20.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:20.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:20.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:20.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:20.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:20.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:20.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:20.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:20.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:20.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:20.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:20.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:20.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:20.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.618][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-13 23:57:20.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-13 23:57:20.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-13 23:57:20.641][biodb::testThat]
biodb.INFO [2025-03-13 23:57:20.643][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-03-13 23:57:20.644][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:57:20.645][biodb::testThat]
biodb.TRACE[2025-03-13 23:57:20.651][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 23:57:20.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 23:57:20.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:20.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:20.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:20.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:20.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:20.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:20.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:20.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:20.714][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:20.723][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:20.726][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-13 23:57:20.728][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:20.732][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-13 23:57:20.736][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:20.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:20.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:20.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:20.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:20.756][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:20.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:20.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:20.784][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:20.794][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:20.796][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-13 23:57:20.799][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:20.804][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-13 23:57:20.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:20.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:20.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:20.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:20.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:20.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:20.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:20.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:20.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:20.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:20.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:20.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:20.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:20.881][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:20.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:20.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:20.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:20.916][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-13 23:57:20.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:20.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:20.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:20.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:20.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:20.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:20.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:20.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:20.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:20.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:20.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:20.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.963][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:20.966][private$selectFields]
biodb.TRACE[2025-03-13 23:57:20.968][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-13 23:57:20.969][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-13 23:57:20.971][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:20.972][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:20.974][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:20.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.978][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.982][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:20.984][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:20.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:20.988][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:20.991][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:20.993][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:20.995][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.001][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.003][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.005][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.007][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-13 23:57:21.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.071][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-13 23:57:21.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:21.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:21.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:21.095][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:21.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:21.099][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:21.104][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[2025-03-13 23:57:21.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.138][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:21.140][private$selectFields]
biodb.TRACE[2025-03-13 23:57:21.143][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-13 23:57:21.148][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-13 23:57:21.151][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:21.153][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.156][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.167][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.169][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.171][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.177][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.180][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:21.182][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:21.184][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.186][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.193][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.195][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-13 23:57:21.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.236][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-13 23:57:21.239][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:21.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:21.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:21.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:21.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:21.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:21.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:21.291][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.315][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:21.317][private$selectFields]
biodb.TRACE[2025-03-13 23:57:21.325][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-13 23:57:21.328][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-13 23:57:21.330][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:21.333][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.343][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.412][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.415][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.418][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.428][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.430][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:21.464][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:21.467][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.478][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.482][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.484][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-13 23:57:21.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:21.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.551][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-13 23:57:21.565][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-13 23:57:21.568][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-13 23:57:21.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:21.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:21.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.628][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:21.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:21.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:21.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:21.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:21.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:21.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:21.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:21.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:21.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:21.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:21.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:21.978][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:21.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:21.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:21.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:21.998][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:22.008][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:22.010][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:22.021][private$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[2025-03-13 23:57:22.442][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[2025-03-13 23:57:22.850][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:22.854][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-03-13 23:57:22.859][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-03-13 23:57:22.867][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[2025-03-13 23:57:22.874][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:22.876][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:22.881][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-13 23:57:23.303][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-13 23:57:23.722][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:23.727][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-03-13 23:57:23.734][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-03-13 23:57:23.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:23.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:23.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:23.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:23.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:23.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:23.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:23.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:23.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:23.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:23.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:23.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:23.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:23.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:23.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:23.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:23.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:23.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:23.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:23.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:23.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:23.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:23.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:23.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:23.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:23.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:23.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:23.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:23.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:23.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:23.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:23.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:23.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:23.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:23.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:23.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:23.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:23.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:23.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:23.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:23.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:23.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:23.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:23.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:23.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:23.861][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:23.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:23.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:23.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:23.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:23.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:23.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:23.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:23.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:23.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:23.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:23.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:23.935][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-13 23:57:23.999][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:24.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:24.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:24.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:24.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:24.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:24.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:24.014][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.026][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:24.027][private$selectFields]
biodb.TRACE[2025-03-13 23:57:24.028][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-13 23:57:24.030][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-13 23:57:24.031][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:24.032][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.034][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.038][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.040][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.042][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.045][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.047][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:24.049][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:24.051][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.053][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.057][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.060][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-13 23:57:24.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.094][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-13 23:57:24.096][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:24.098][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:24.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:24.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:24.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:24.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:24.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:24.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.242][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:24.247][private$selectFields]
biodb.TRACE[2025-03-13 23:57:24.249][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-13 23:57:24.251][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-13 23:57:24.253][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:24.255][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.259][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.262][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.263][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.265][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.267][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.268][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:24.286][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:24.288][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.290][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.292][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.294][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-13 23:57:24.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.320][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-13 23:57:24.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:24.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:24.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:24.333][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:24.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:24.337][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:24.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:24.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.371][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:24.373][private$selectFields]
biodb.TRACE[2025-03-13 23:57:24.376][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-13 23:57:24.379][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-13 23:57:24.384][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:24.386][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.388][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.393][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.395][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.398][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.402][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.404][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:24.407][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:24.409][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.411][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.415][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.417][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-13 23:57:24.419][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.444][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-13 23:57:24.447][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-13 23:57:24.449][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-13 23:57:24.468][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-13 23:57:24.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-13 23:57:24.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-13 23:57:24.485][biodb::testThat]
biodb.INFO [2025-03-13 23:57:24.487][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-03-13 23:57:24.489][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:57:24.491][biodb::testThat]
biodb.TRACE[2025-03-13 23:57:24.497][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 23:57:24.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 23:57:24.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.504][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:24.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:24.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:24.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:24.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:24.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:24.547][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:24.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:24.556][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:24.562][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:24.564][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-13 23:57:24.567][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:24.570][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-13 23:57:24.575][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:24.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:24.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:24.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:24.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:24.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:24.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:24.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.690][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:24.717][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:24.726][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:24.731][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-13 23:57:24.734][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:24.740][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-13 23:57:24.756][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:24.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:24.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:24.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:24.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:24.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:24.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:24.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:24.805][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:24.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:24.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:24.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:24.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:24.825][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:24.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:24.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:24.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:24.860][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-13 23:57:24.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:24.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:24.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:24.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:24.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:24.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:24.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:24.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.906][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:24.907][private$selectFields]
biodb.TRACE[2025-03-13 23:57:24.909][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-13 23:57:24.910][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-13 23:57:24.911][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:24.912][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.914][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.917][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.919][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.921][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.925][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.927][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:24.929][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:24.931][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.934][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.938][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.940][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-13 23:57:24.943][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:24.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:24.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:24.979][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-13 23:57:24.981][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:24.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:24.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:25.004][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:25.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:25.009][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:25.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:25.014][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.033][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:25.035][private$selectFields]
biodb.TRACE[2025-03-13 23:57:25.038][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-13 23:57:25.040][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-13 23:57:25.042][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:25.044][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.047][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.052][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.054][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.057][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.061][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.063][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:25.066][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:25.068][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.070][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.071][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.073][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.074][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-13 23:57:25.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.101][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-13 23:57:25.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:25.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:25.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:25.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:25.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:25.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:25.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:25.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.145][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:25.147][private$selectFields]
biodb.TRACE[2025-03-13 23:57:25.149][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-13 23:57:25.151][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-13 23:57:25.153][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:25.156][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.159][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.164][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.166][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.167][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.170][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.172][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:25.175][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:25.177][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.180][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.184][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.187][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-13 23:57:25.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.239][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-13 23:57:25.242][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-13 23:57:25.244][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-13 23:57:25.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:25.343][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:25.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:25.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:25.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:25.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:25.368][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:25.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:25.396][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:25.409][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:25.412][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-13 23:57:25.417][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:25.420][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-13 23:57:25.428][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:25.440][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:25.442][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-13 23:57:25.444][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:25.446][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-13 23:57:25.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:25.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:25.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:25.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:25.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:25.463][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:25.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:25.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:25.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:25.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:25.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:25.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:25.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:25.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:25.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:25.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:25.631][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:25.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:25.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:25.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:25.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:25.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:25.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:25.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.679][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:25.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:25.689][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-13 23:57:25.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:25.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:25.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:25.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:25.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:25.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:25.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:25.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.753][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:25.755][private$selectFields]
biodb.TRACE[2025-03-13 23:57:25.757][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-13 23:57:25.759][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-13 23:57:25.761][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:25.764][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.766][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.771][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.774][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.776][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.780][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.790][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:25.792][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:25.795][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.797][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.810][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.812][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-13 23:57:25.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.853][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-13 23:57:25.856][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:25.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:25.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:25.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:25.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:25.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:25.894][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.TRACE[2025-03-13 23:57:25.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:25.965][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:25.967][private$selectFields]
biodb.TRACE[2025-03-13 23:57:25.970][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-13 23:57:25.972][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-13 23:57:25.974][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:25.986][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.989][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:25.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:25.993][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.012][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.026][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.028][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.030][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.032][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:26.035][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:26.039][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.041][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.045][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.048][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-13 23:57:26.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.092][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-13 23:57:26.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:26.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:26.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:26.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:26.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:26.119][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:26.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:26.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.164][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:26.166][private$selectFields]
biodb.TRACE[2025-03-13 23:57:26.208][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-13 23:57:26.222][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-13 23:57:26.224][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:26.227][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.229][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.237][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.239][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.253][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.268][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.270][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:26.273][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:26.277][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.280][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.284][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.287][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-13 23:57:26.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.343][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-13 23:57:26.345][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-13 23:57:26.349][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-13 23:57:26.393][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-13 23:57:26.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-13 23:57:26.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-13 23:57:26.415][biodb::testThat]
biodb.INFO [2025-03-13 23:57:26.430][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-03-13 23:57:26.433][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:57:26.435][biodb::testThat]
biodb.TRACE[2025-03-13 23:57:26.453][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-13 23:57:26.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-13 23:57:26.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.490][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:26.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:26.572][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:26.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:26.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:26.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:26.601][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:26.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:26.610][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:26.621][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:26.634][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-13 23:57:26.637][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:26.642][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-13 23:57:26.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:26.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:26.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:26.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:26.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:26.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:26.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:26.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:26.735][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:26.741][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:26.750][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-13 23:57:26.753][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:26.756][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-13 23:57:26.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:26.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:26.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:26.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:26.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:26.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:26.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:26.825][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:26.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:26.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:26.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:26.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:26.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:26.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:26.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:26.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:26.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:26.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:26.947][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-13 23:57:26.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:26.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:26.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:26.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:26.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:26.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:26.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:26.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:26.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:26.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.019][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:27.021][private$selectFields]
biodb.TRACE[2025-03-13 23:57:27.033][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-13 23:57:27.035][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-13 23:57:27.038][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:27.045][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.048][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.053][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.059][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.062][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.067][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.079][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:27.082][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:27.084][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.087][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.100][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.103][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-13 23:57:27.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.202][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.221][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-13 23:57:27.223][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:27.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:27.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:27.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:27.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:27.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:27.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:27.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.334][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:27.336][private$selectFields]
biodb.TRACE[2025-03-13 23:57:27.359][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-13 23:57:27.362][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-13 23:57:27.366][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:27.368][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.380][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.385][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.388][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.391][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.397][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.413][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:27.415][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:27.418][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.421][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.439][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.441][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.444][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-13 23:57:27.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.506][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-13 23:57:27.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:27.521][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:27.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:27.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:27.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:27.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:27.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:27.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.609][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:27.611][private$selectFields]
biodb.TRACE[2025-03-13 23:57:27.624][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-13 23:57:27.626][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-13 23:57:27.628][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:27.630][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.643][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.648][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.650][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.661][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.666][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.668][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:27.680][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:27.682][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.685][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.689][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.702][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-13 23:57:27.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:27.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.767][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-13 23:57:27.770][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-13 23:57:27.782][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-13 23:57:27.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:27.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:27.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:27.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:27.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:27.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:27.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:27.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:27.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:27.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:27.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:27.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:28.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:28.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:28.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:28.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:28.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:28.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:28.048][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:28.068][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:28.071][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-13 23:57:28.086][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:28.089][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-13 23:57:28.106][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:28.124][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:28.127][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-13 23:57:28.130][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:28.145][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-13 23:57:28.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:28.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:28.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:28.188][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:28.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:28.193][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:28.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:28.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:28.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:28.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:28.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:28.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:28.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:28.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:28.269][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:28.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:28.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:28.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:28.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:28.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:28.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:28.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:28.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:28.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:28.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:28.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:28.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:28.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:28.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:28.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:28.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:28.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:28.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:28.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:28.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:28.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:28.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:28.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:28.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:28.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:28.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:28.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:28.506][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-13 23:57:28.509][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:28.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:28.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:28.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:28.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:28.549][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:28.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:28.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.606][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:28.609][private$selectFields]
biodb.TRACE[2025-03-13 23:57:28.611][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-13 23:57:28.627][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-13 23:57:28.631][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:28.633][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.647][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.652][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.654][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.667][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.672][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.674][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:28.687][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:28.690][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.693][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.709][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.711][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-13 23:57:28.714][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.778][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-13 23:57:28.792][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:28.794][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:28.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:28.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:28.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:28.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:28.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:28.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.863][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.883][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:28.886][private$selectFields]
biodb.TRACE[2025-03-13 23:57:28.888][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-13 23:57:28.891][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-13 23:57:28.902][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:28.904][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.907][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.923][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.926][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.929][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.945][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.948][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:28.951][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:28.968][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.972][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:28.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:28.989][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:28.993][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-13 23:57:28.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:29.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:29.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:29.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:29.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:29.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:29.070][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-13 23:57:29.073][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:29.076][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:29.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:29.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:29.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:29.123][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:29.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:29.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:29.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:29.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:29.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:29.178][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:29.180][private$selectFields]
biodb.TRACE[2025-03-13 23:57:29.182][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-13 23:57:29.192][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-13 23:57:29.194][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:29.197][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.199][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:29.214][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:29.217][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.219][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:29.238][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:29.240][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:29.242][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-13 23:57:29.255][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.258][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:29.262][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:29.264][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-13 23:57:29.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:29.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:29.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:29.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:29.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:29.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:29.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:29.327][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-13 23:57:29.328][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-13 23:57:29.329][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-13 23:57:29.394][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-13 23:57:29.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-13 23:57:29.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:29.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-13 23:57:29.414][biodb::testThat]
biodb.INFO [2025-03-13 23:57:29.428][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-03-13 23:57:29.430][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:57:29.432][biodb::testThat]
biodb.DEBUG[2025-03-13 23:57:29.436][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-13 23:57:29.439][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:57:29.442][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-13 23:57:29.445][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:57:29.449][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:57:29.459][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:57:29.462][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:57:29.464][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:57:29.466][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:57:29.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:29.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:29.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:29.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:29.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:29.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:29.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:29.518][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-03-13 23:57:29.525][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:29.536][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:29.540][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-03-13 23:57:30.012][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-03-13 23:57:30.420][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:30.424][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-03-13 23:57:30.433][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-03-13 23:57:30.439][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-03-13 23:57:30.443][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:57:30.446][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:57:30.449][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:57:30.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:30.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:30.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:30.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:30.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:30.486][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:30.488][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.TRACE[2025-03-13 23:57:30.493][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:30.496][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:30.498][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.500][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:30.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:30.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.512][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:30.515][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:30.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.519][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.521][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:30.524][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:30.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.528][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.531][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:30.533][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:30.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.537][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.540][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:30.542][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:30.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.553][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.556][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:30.559][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:30.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.569][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.572][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:30.574][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:30.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.588][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.590][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:30.593][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:30.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.604][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.607][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:30.610][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:30.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.624][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.627][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:30.630][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:30.638][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.640][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.643][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:30.654][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:30.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.659][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:30.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:30.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:30.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:30.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:30.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:30.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:30.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:30.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:30.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:30.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:30.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:30.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:30.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:30.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:30.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:30.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:30.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:30.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:30.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:30.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:30.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:30.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:30.829][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-03-13 23:57:30.832][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-13 23:57:30.866][biodb::testThat]
biodb.INFO [2025-03-13 23:57:30.869][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-03-13 23:57:30.872][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:57:30.874][biodb::testThat]
biodb.DEBUG[2025-03-13 23:57:31.104][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-03-13 23:57:31.111][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-03-13 23:57:31.114][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-03-13 23:57:31.118][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-03-13 23:57:31.121][cch$loadFileContent] file.exist = [3]: "FALSE, TRUE, FALSE".
biodb.TRACE[2025-03-13 23:57:31.125][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml".
biodb.DEBUG[2025-03-13 23:57:31.127][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:57:31.130][conn$getEntryContent] 2 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:57:31.132][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:57:31.134][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:57:31.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:31.151][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:31.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:31.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:31.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:31.186][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:31.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:31.191][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-03-13 23:57:31.207][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:31.210][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:31.223][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-03-13 23:57:31.641][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-03-13 23:57:32.091][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:32.095][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-03-13 23:57:32.104][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-03-13 23:57:32.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:32.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:32.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:32.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:32.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:32.124][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:32.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:32.127][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-03-13 23:57:32.134][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:32.137][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:32.141][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-03-13 23:57:32.572][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-03-13 23:57:33.014][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:33.019][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-03-13 23:57:33.032][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-03-13 23:57:33.121][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-03-13 23:57:33.126][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:57:33.129][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-03-13 23:57:33.131][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-03-13 23:57:33.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:33.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:33.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:33.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:33.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:33.153][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:33.155][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.TRACE[2025-03-13 23:57:33.160][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:33.162][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:33.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.167][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:33.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:33.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.179][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:33.192][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:33.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.196][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.199][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:33.206][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:33.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.209][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.211][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:33.213][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:33.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.220][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.223][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:33.226][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:33.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.230][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.233][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:33.235][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:33.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.240][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.243][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:33.245][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:33.248][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.251][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.258][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:33.260][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:33.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.264][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.268][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:33.275][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:33.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.280][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.284][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:33.286][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:33.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.290][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.292][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:33.294][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:33.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.300][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:33.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:33.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:33.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:33.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:33.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:33.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:33.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:33.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:33.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:33.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:33.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:33.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:33.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:33.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:33.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:33.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:33.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:33.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:33.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:33.434][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:33.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:33.441][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:33.444][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:33.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.447][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:33.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:33.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.466][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:33.470][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:33.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.481][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.483][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:33.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:33.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.494][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:33.496][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:33.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.507][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.510][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:33.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:33.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.520][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:33.523][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:33.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.527][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.530][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:33.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:33.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.562][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:33.564][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:33.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.569][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:33.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:33.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.589][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:33.591][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:33.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.596][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.602][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:33.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:33.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.619][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:33.622][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:33.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.627][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.630][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:33.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:33.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.679][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:33.682][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:33.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.687][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.691][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:33.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:33.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.703][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:33.706][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:33.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.716][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:33.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:33.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.730][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:33.736][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:33.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.740][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.744][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:33.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:33.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.761][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:33.771][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:33.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.782][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.786][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:33.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:33.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:33.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:33.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:33.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:33.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:33.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:33.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:33.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:33.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:33.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:33.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:33.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:33.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:33.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:33.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:33.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:33.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:33.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:33.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:33.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:33.935][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:33.937][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.TRACE[2025-03-13 23:57:33.943][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:33.955][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:33.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.961][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:33.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:33.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:33.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:33.982][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:33.985][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:33.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.005][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.009][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:34.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:34.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.062][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:34.065][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:34.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.083][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.086][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:34.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:34.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.105][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:34.115][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:34.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.120][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.123][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:34.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:34.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.154][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:34.157][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:34.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.163][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.174][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:34.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:34.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.195][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:34.198][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:34.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.214][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.217][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:34.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:34.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.237][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:34.240][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:34.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.257][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.260][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:34.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:34.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.284][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:34.297][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:34.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.302][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:34.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:34.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.334][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:34.337][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:34.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.342][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:34.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:34.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.377][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:34.380][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:34.382][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.394][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.397][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:34.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:34.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.418][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:34.430][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:34.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.436][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.439][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:34.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:34.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:34.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:34.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:34.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:34.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:34.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:34.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:34.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:34.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:34.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:34.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:34.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:34.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:34.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:34.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:34.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:34.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:34.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:34.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:34.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:34.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:34.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:34.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:34.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:34.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:34.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:34.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:34.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:34.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:34.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:34.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:34.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:34.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:34.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:34.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:34.814][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-03-13 23:57:34.816][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-13 23:57:34.819][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-03-13 23:57:34.892][biodb::testThat]
biodb.INFO [2025-03-13 23:57:34.894][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-03-13 23:57:34.900][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:57:34.903][biodb::testThat]
biodb.INFO [2025-03-13 23:57:35.039][biodb::testThat]
biodb.INFO [2025-03-13 23:57:35.044][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-03-13 23:57:35.046][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:57:35.058][biodb::testThat]
biodb.INFO [2025-03-13 23:57:35.085][biodb::testThat]
biodb.INFO [2025-03-13 23:57:35.090][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-03-13 23:57:35.092][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:57:35.094][biodb::testThat]
biodb.DEBUG[2025-03-13 23:57:35.103][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[2025-03-13 23:57:35.112][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:35.114][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:35.118][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-03-13 23:57:35.621][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-03-13 23:57:36.129][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:36.133][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-03-13 23:57:36.151][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-03-13 23:57:36.213][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:36.225][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:36.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:36.229][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:36.232][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:36.244][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:36.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:36.249][ef$get] fields variable is a list.
biodb.INFO [2025-03-13 23:57:36.253][biodb::testThat]
biodb.INFO [2025-03-13 23:57:36.263][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-03-13 23:57:36.265][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:57:36.267][biodb::testThat]
biodb.ERROR[2025-03-13 23:57:36.331][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-03-13 23:57:36.445][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-03-13 23:57:36.507][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-13 23:57:36.509][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-13 23:57:36.512][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-13 23:57:36.513][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-13 23:57:36.526][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:36.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:36.530][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:36.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:36.534][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:36.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-13 23:57:36.600][biodb::testContext]
biodb.INFO [2025-03-13 23:57:36.602][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-13 23:57:36.604][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-03-13 23:57:36.606][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-13 23:57:36.609][biodb::testContext]
biodb.INFO [2025-03-13 23:57:36.624][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-13 23:57:36.629][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-13 23:57:36.645][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 23:57:36.648][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-13 23:57:36.661][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-13 23:57:36.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:36.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:36.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:36.681][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-13 23:57:36.683][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-13 23:57:36.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:36.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:36.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:36.701][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-13 23:57:36.703][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-13 23:57:36.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:36.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:36.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:36.722][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-13 23:57:36.724][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-13 23:57:36.727][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-13 23:57:36.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:36.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:36.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:36.751][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-13 23:57:36.755][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-13 23:57:36.767][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-13 23:57:36.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:36.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:36.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:36.783][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-13 23:57:36.786][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-13 23:57:36.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:36.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:36.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:36.805][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-13 23:57:36.807][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-13 23:57:36.809][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-13 23:57:36.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:36.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:36.828][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[2025-03-13 23:57:36.830][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-13 23:57:36.832][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-13 23:57:36.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:36.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:36.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:36.853][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-13 23:57:36.866][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-13 23:57:36.869][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-13 23:57:36.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:36.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:36.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:36.887][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-13 23:57:36.890][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-13 23:57:36.892][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-13 23:57:36.894][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-13 23:57:36.904][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-13 23:57:36.907][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-13 23:57:36.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:36.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:36.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:36.926][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-13 23:57:36.929][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-13 23:57:36.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:36.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:36.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:36.949][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-13 23:57:36.952][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-13 23:57:36.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:36.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:36.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:36.961][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-13 23:57:36.977][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-13 23:57:36.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:36.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:36.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:36.985][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-13 23:57:36.997][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-13 23:57:37.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.023][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-13 23:57:37.026][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-13 23:57:37.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.042][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-13 23:57:37.045][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-13 23:57:37.066][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-13 23:57:37.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.075][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-13 23:57:37.077][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-13 23:57:37.079][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-13 23:57:37.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.085][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[2025-03-13 23:57:37.091][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-13 23:57:37.095][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:37.098][self$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[2025-03-13 23:57:37.109][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:37.112][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:57:37.115][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:37.119][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:57:37.121][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:37.123][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 23:57:37.125][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-13 23:57:37.127][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:57:37.130][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:37.142][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-13 23:57:37.144][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:57:37.146][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:37.148][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:37.150][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 23:57:37.150][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-13 23:57:37.150][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-13 23:57:37.150][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-13 23:57:37.150][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-13 23:57:37.156][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 23:57:37.158][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:37.173][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:37.176][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:57:37.178][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:37.180][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:37.182][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:57:37.184][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:37.187][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:57:37.189][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:57:37.191][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:37.194][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:37.196][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-13 23:57:37.199][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:37.201][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-13 23:57:37.203][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:37.205][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:57:37.208][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:37.210][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:57:37.212][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:37.214][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 23:57:37.217][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-13 23:57:37.219][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:57:37.222][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:37.224][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-13 23:57:37.226][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:57:37.229][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:37.232][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:37.235][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 23:57:37.235][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-13 23:57:37.235][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-13 23:57:37.235][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-13 23:57:37.235][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-13 23:57:37.237][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 23:57:37.239][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:37.241][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:37.243][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:57:37.245][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:37.246][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:37.248][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:57:37.249][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:37.250][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:57:37.252][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:57:37.253][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:37.254][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:37.257][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-13 23:57:37.261][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:37.263][self$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[2025-03-13 23:57:37.264][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:37.266][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:57:37.267][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:37.268][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:57:37.270][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:37.271][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 23:57:37.272][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-13 23:57:37.277][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:57:37.280][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:37.282][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-13 23:57:37.283][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:57:37.284][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:37.286][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:37.287][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:37.291][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 23:57:37.293][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:37.294][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:37.296][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:57:37.298][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:37.299][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:37.302][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:57:37.304][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:37.306][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:57:37.308][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:57:37.310][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:37.313][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:37.316][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-13 23:57:37.321][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:37.324][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-13 23:57:37.326][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:37.328][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:57:37.331][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:37.334][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:57:37.336][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:37.338][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 23:57:37.339][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-13 23:57:37.341][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:57:37.343][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:37.345][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-13 23:57:37.347][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:57:37.350][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:37.352][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:37.354][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:37.356][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 23:57:37.357][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:37.359][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:37.361][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:57:37.364][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:37.367][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:37.368][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:57:37.370][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:37.371][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:57:37.372][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:57:37.373][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:37.375][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:37.377][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 23:57:37.379][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.381][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[2025-03-13 23:57:37.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.415][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[2025-03-13 23:57:37.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.462][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[2025-03-13 23:57:37.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.506][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[2025-03-13 23:57:37.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.539][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-13 23:57:37.555][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-13 23:57:37.557][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-13 23:57:37.561][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-13 23:57:37.564][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-13 23:57:37.568][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-13 23:57:37.571][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-13 23:57:37.575][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-13 23:57:37.579][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-13 23:57:37.582][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-13 23:57:37.585][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-13 23:57:37.587][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-13 23:57:37.589][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-13 23:57:37.593][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-13 23:57:37.597][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-13 23:57:37.600][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-13 23:57:37.608][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-13 23:57:37.612][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-13 23:57:37.615][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-13 23:57:37.618][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-13 23:57:37.623][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-13 23:57:37.626][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-13 23:57:37.630][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-13 23:57:37.633][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-13 23:57:37.636][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-13 23:57:37.639][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-13 23:57:37.643][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-13 23:57:37.646][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-13 23:57:37.654][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-13 23:57:37.657][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-13 23:57:37.660][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-13 23:57:37.664][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-13 23:57:37.667][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-13 23:57:37.670][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-13 23:57:37.673][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-13 23:57:37.676][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-13 23:57:37.680][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-13 23:57:37.683][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-13 23:57:37.685][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-13 23:57:37.687][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-13 23:57:37.689][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-13 23:57:37.692][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-13 23:57:37.698][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-13 23:57:37.700][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-13 23:57:37.702][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-13 23:57:37.704][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-13 23:57:37.706][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-13 23:57:37.712][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-13 23:57:37.715][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-13 23:57:37.718][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-13 23:57:37.722][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-13 23:57:37.725][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-13 23:57:37.727][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-13 23:57:37.729][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-13 23:57:37.731][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-13 23:57:37.734][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-13 23:57:37.738][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-13 23:57:37.742][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-13 23:57:37.746][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-13 23:57:37.749][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-13 23:57:37.754][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-13 23:57:37.757][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-13 23:57:37.761][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-13 23:57:37.763][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-13 23:57:37.766][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-13 23:57:37.770][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-13 23:57:37.773][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-13 23:57:37.776][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-13 23:57:37.784][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-13 23:57:37.787][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-13 23:57:37.791][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-13 23:57:37.794][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-13 23:57:37.797][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-13 23:57:37.800][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-13 23:57:37.803][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-13 23:57:37.805][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-13 23:57:37.808][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-13 23:57:37.810][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-13 23:57:37.813][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-13 23:57:37.816][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-13 23:57:37.819][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-13 23:57:37.822][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-13 23:57:37.825][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-13 23:57:37.829][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-13 23:57:37.832][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-13 23:57:37.834][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 23:57:37.835][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.839][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.841][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[2025-03-13 23:57:37.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:37.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:37.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:37.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:37.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:37.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:37.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:37.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:37.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.894][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[2025-03-13 23:57:37.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:37.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:37.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:37.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:37.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:37.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:37.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:37.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:37.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:37.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:37.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:37.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:37.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:37.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:37.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:37.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:37.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:37.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:37.995][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.DEBUG[2025-03-13 23:57:37.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:37.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:37.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:38.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:38.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:38.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:38.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:38.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:38.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:38.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:38.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:38.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:38.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:38.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:38.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:38.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:38.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:38.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:38.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:38.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:38.024][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[2025-03-13 23:57:38.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:38.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:38.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:38.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:38.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:38.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:38.037][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[2025-03-13 23:57:38.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:38.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:38.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:38.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:38.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:38.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:38.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:38.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:38.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:38.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:38.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:38.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:38.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:38.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:38.079][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-13 23:57:38.082][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-13 23:57:38.087][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:38.088][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-13 23:57:38.089][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:38.091][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:57:38.092][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:38.093][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:57:38.094][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:38.096][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-13 23:57:38.098][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-13 23:57:38.101][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:57:38.103][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:38.105][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-13 23:57:38.107][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:57:38.109][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-13 23:57:38.109][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-13 23:57:38.109][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-13 23:57:38.109][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-13 23:57:38.109][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-13 23:57:38.109][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-13 23:57:38.109][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-13 23:57:38.109][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-13 23:57:38.109][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-13 23:57:38.109][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-13 23:57:38.109][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-13 23:57:38.111][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:38.112][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 23:57:38.112][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-13 23:57:38.112][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-13 23:57:38.115][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-13 23:57:38.117][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:38.119][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:38.121][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:57:38.122][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:38.123][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:38.125][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:57:38.126][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:57:38.126][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-13 23:57:38.128][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:57:38.130][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:57:38.132][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:38.134][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-13 23:57:38.134][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-13 23:57:38.136][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-13 23:57:38.139][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-13 23:57:38.141][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-13 23:57:38.143][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-13 23:57:38.148][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-13 23:57:38.150][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-13 23:57:38.155][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-13 23:57:38.157][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-13 23:57:38.161][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-13 23:57:38.163][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-13 23:57:38.165][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 23:57:38.166][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 23:57:38.169][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-13 23:57:38.170][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-13 23:57:38.173][biodb::testThat]
biodb.INFO [2025-03-13 23:57:38.175][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-03-13 23:57:38.177][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:57:38.178][biodb::testThat]
biodb.DEBUG[2025-03-13 23:57:38.184][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-13 23:57:38.195][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:38.198][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-13 23:57:38.201][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:38.231][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-13 23:57:38.236][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:38.240][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:38.242][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-13 23:57:38.247][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:38.250][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-13 23:57:38.252][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:38.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:38.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:38.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:38.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:38.266][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:38.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:38.269][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:38.276][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:38.278][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-13 23:57:38.279][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:38.282][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-13 23:57:38.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:38.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:38.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:38.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:38.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:38.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:38.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:38.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:38.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:38.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:38.350][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:38.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:38.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:38.355][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[2025-03-13 23:57:38.362][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:38.369][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:38.371][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-13 23:57:38.373][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:38.374][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-13 23:57:38.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:38.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:38.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:38.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:38.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:38.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:38.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:38.401][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:38.405][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:38.407][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-13 23:57:38.408][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:38.415][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-13 23:57:38.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:38.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:38.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:38.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:38.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:38.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:38.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:38.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:38.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:38.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:38.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:38.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:38.450][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:38.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:38.459][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:38.463][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:38.468][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-13 23:57:38.470][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:38.471][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-13 23:57:38.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:38.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:38.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:38.485][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:38.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:38.489][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:38.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:38.493][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:38.499][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:38.501][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-13 23:57:38.502][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:38.504][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-13 23:57:38.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:38.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:38.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:38.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:38.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:38.526][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:38.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:38.531][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:38.535][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:38.539][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2025-03-13 23:57:38.541][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:38.543][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2025-03-13 23:57:38.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:38.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:38.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:38.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:38.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:38.560][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:38.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-13 23:57:38.616][biodb::testThat]
biodb.INFO [2025-03-13 23:57:38.618][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-03-13 23:57:38.620][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:57:38.622][biodb::testThat]
biodb.DEBUG[2025-03-13 23:57:38.629][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:38.635][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:38.637][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:38.642][private$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[2025-03-13 23:57:39.046][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[2025-03-13 23:57:39.456][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:39.460][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-03-13 23:57:39.473][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-03-13 23:57:39.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:39.479][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:39.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:39.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:39.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:39.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:39.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:39.504][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[2025-03-13 23:57:39.508][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:39.510][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:39.513][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-13 23:57:39.925][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-13 23:57:40.332][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:40.336][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-03-13 23:57:40.346][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-03-13 23:57:40.351][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:40.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:40.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:40.366][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:40.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:40.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-13 23:57:40.384][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-13 23:57:40.386][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-13 23:57:40.389][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-13 23:57:40.391][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-13 23:57:40.393][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:40.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:40.397][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:40.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:40.401][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-13 23:57:40.411][biodb::testContext]
biodb.INFO [2025-03-13 23:57:40.413][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-13 23:57:40.415][biodb::testContext] Test context - Test web services
biodb.INFO [2025-03-13 23:57:40.418][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-13 23:57:40.420][biodb::testContext]
biodb.INFO [2025-03-13 23:57:40.424][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-13 23:57:40.428][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-13 23:57:40.436][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 23:57:40.438][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-13 23:57:40.440][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-13 23:57:40.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:40.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:40.448][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-13 23:57:40.451][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-13 23:57:40.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:40.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:40.466][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-13 23:57:40.468][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-13 23:57:40.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:40.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:40.489][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-13 23:57:40.492][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-13 23:57:40.494][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-13 23:57:40.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:40.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:40.511][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-13 23:57:40.514][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-13 23:57:40.517][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-13 23:57:40.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:40.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:40.525][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-13 23:57:40.528][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-13 23:57:40.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:40.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:40.543][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-13 23:57:40.545][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-13 23:57:40.548][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-13 23:57:40.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:40.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:40.556][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-13 23:57:40.559][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-13 23:57:40.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:40.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:40.569][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-13 23:57:40.571][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-13 23:57:40.573][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-13 23:57:40.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:40.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.578][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[2025-03-13 23:57:40.594][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-13 23:57:40.596][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-13 23:57:40.599][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-13 23:57:40.602][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-13 23:57:40.604][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-13 23:57:40.606][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-13 23:57:40.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:40.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:40.621][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-13 23:57:40.626][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-13 23:57:40.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:40.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.632][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.DEBUG[2025-03-13 23:57:40.638][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-13 23:57:40.640][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-13 23:57:40.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:40.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:40.657][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-13 23:57:40.659][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-13 23:57:40.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:40.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:40.672][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-13 23:57:40.674][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-13 23:57:40.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:40.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:40.685][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-13 23:57:40.688][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-13 23:57:40.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:40.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.696][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[2025-03-13 23:57:40.698][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-13 23:57:40.701][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-13 23:57:40.851][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-13 23:57:40.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:40.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:40.858][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-13 23:57:40.860][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-13 23:57:40.862][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-13 23:57:40.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:40.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:40.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:40.871][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-13 23:57:40.879][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:40.881][self$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[2025-03-13 23:57:40.883][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:40.887][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:57:40.890][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:40.893][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:57:40.895][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:40.898][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 23:57:40.900][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-13 23:57:40.902][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:57:40.916][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:40.919][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-13 23:57:40.944][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:57:40.946][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:40.948][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:40.950][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 23:57:40.950][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-13 23:57:40.950][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-13 23:57:40.950][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-13 23:57:40.950][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-13 23:57:40.958][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 23:57:40.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:40.962][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:40.964][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:57:40.966][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:40.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:40.977][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:57:40.981][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:40.983][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:57:40.985][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:57:40.992][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:40.994][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:40.996][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-13 23:57:40.999][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:41.002][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-13 23:57:41.006][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:41.009][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:57:41.011][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:41.017][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:57:41.019][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:41.021][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 23:57:41.023][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-13 23:57:41.025][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:57:41.028][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:41.030][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-13 23:57:41.038][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:57:41.041][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:41.042][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:41.043][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 23:57:41.043][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-13 23:57:41.043][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-13 23:57:41.043][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-13 23:57:41.043][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-13 23:57:41.045][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 23:57:41.046][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:41.047][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:41.051][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:57:41.054][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:41.056][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:41.058][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:57:41.059][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:41.061][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:57:41.063][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:57:41.065][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:41.067][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:41.070][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-13 23:57:41.076][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:41.078][self$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[2025-03-13 23:57:41.079][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:41.080][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:57:41.082][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:41.083][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:57:41.086][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:41.089][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 23:57:41.091][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-13 23:57:41.094][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:57:41.096][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:41.098][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-13 23:57:41.100][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:57:41.103][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:41.110][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:41.113][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:41.115][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 23:57:41.118][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:41.120][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:41.124][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:57:41.126][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:41.128][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:41.130][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:57:41.132][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:41.133][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:57:41.135][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:57:41.137][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:41.139][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:41.147][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-13 23:57:41.151][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:41.153][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-13 23:57:41.158][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:41.161][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:57:41.163][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:41.165][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:57:41.171][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:41.174][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 23:57:41.176][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-13 23:57:41.178][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:57:41.185][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:41.188][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-13 23:57:41.190][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:57:41.193][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:41.201][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:41.205][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:41.207][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 23:57:41.210][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:41.217][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:41.220][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:57:41.222][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:41.227][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:41.233][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:57:41.235][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:41.238][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:57:41.240][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:57:41.246][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:41.249][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:41.253][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 23:57:41.255][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:41.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.276][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[2025-03-13 23:57:41.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:41.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:41.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:41.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:41.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:41.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:41.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.372][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[2025-03-13 23:57:41.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.385][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[2025-03-13 23:57:41.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:41.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.406][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[2025-03-13 23:57:41.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:41.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:41.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:41.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:41.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:41.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.497][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[2025-03-13 23:57:41.507][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-13 23:57:41.519][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-13 23:57:41.527][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-13 23:57:41.530][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-13 23:57:41.539][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-13 23:57:41.543][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-13 23:57:41.546][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-13 23:57:41.558][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-13 23:57:41.561][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-13 23:57:41.566][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-13 23:57:41.570][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-13 23:57:41.573][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-13 23:57:41.585][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-13 23:57:41.589][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-13 23:57:41.592][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-13 23:57:41.600][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-13 23:57:41.603][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-13 23:57:41.607][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-13 23:57:41.614][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-13 23:57:41.618][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-13 23:57:41.625][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-13 23:57:41.628][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-13 23:57:41.632][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-13 23:57:41.638][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-13 23:57:41.643][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-13 23:57:41.647][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-13 23:57:41.655][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-13 23:57:41.659][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-13 23:57:41.664][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-13 23:57:41.667][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-13 23:57:41.671][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-13 23:57:41.676][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-13 23:57:41.679][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-13 23:57:41.683][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-13 23:57:41.690][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-13 23:57:41.694][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-13 23:57:41.697][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-13 23:57:41.703][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-13 23:57:41.707][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-13 23:57:41.711][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-13 23:57:41.717][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-13 23:57:41.720][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-13 23:57:41.723][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-13 23:57:41.730][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-13 23:57:41.734][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-13 23:57:41.737][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-13 23:57:41.744][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-13 23:57:41.748][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-13 23:57:41.752][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-13 23:57:41.758][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-13 23:57:41.761][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-13 23:57:41.767][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-13 23:57:41.772][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-13 23:57:41.775][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-13 23:57:41.779][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-13 23:57:41.782][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-13 23:57:41.785][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-13 23:57:41.790][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-13 23:57:41.793][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-13 23:57:41.797][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-13 23:57:41.807][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-13 23:57:41.811][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-13 23:57:41.814][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-13 23:57:41.820][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-13 23:57:41.824][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-13 23:57:41.828][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-13 23:57:41.832][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-13 23:57:41.836][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-13 23:57:41.840][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-13 23:57:41.845][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-13 23:57:41.848][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-13 23:57:41.853][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-13 23:57:41.858][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-13 23:57:41.861][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-13 23:57:41.866][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-13 23:57:41.872][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-13 23:57:41.876][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-13 23:57:41.881][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-13 23:57:41.884][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-13 23:57:41.888][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-13 23:57:41.892][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-13 23:57:41.896][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-13 23:57:41.899][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-13 23:57:41.903][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-13 23:57:41.909][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-13 23:57:41.912][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 23:57:41.914][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.919][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.922][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[2025-03-13 23:57:41.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:41.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:41.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:41.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:41.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:41.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:41.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:41.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:41.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.968][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[2025-03-13 23:57:41.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:41.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:41.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:41.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:41.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:41.993][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[2025-03-13 23:57:41.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:41.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:41.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:42.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:42.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:42.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:42.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:42.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:42.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:42.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:42.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:42.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:42.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:42.023][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[2025-03-13 23:57:42.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:42.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:42.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:42.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:42.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:42.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:42.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:42.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:42.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:42.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:42.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:42.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:42.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:42.055][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[2025-03-13 23:57:42.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:42.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:42.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:42.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:42.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:42.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:42.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:42.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:42.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:42.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:42.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:42.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:42.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:42.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:42.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:42.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:42.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:42.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:42.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:42.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:42.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:42.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:42.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:42.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:42.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:42.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:42.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:42.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:42.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:42.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:42.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:42.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:42.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:42.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:42.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:42.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:42.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:42.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:42.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:42.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:42.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:42.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:42.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:42.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:42.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:42.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:42.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:42.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:42.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:42.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:42.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:42.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:42.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:42.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:42.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:42.199][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[2025-03-13 23:57:42.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:42.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:42.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:42.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:42.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:42.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:42.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:42.229][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-13 23:57:42.233][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-13 23:57:42.236][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:42.238][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-13 23:57:42.239][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:42.241][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:57:42.244][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:42.246][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:57:42.248][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:42.251][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-13 23:57:42.255][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-13 23:57:42.258][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:57:42.261][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:42.264][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-13 23:57:42.266][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:57:42.269][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-13 23:57:42.269][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-13 23:57:42.269][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-13 23:57:42.269][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-13 23:57:42.269][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-13 23:57:42.269][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-13 23:57:42.269][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-13 23:57:42.269][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-13 23:57:42.269][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-13 23:57:42.269][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-13 23:57:42.269][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-13 23:57:42.273][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:42.275][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 23:57:42.275][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-13 23:57:42.275][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-13 23:57:42.276][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-13 23:57:42.278][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:42.279][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:42.280][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:57:42.281][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:42.282][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:42.284][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:57:42.288][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:57:42.288][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-13 23:57:42.293][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:57:42.296][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:57:42.346][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:42.350][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-13 23:57:42.350][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-13 23:57:42.357][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-13 23:57:42.363][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-13 23:57:42.427][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-13 23:57:42.435][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-13 23:57:42.438][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-13 23:57:42.441][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-13 23:57:42.450][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-13 23:57:42.452][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-13 23:57:42.455][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-13 23:57:42.458][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-13 23:57:42.461][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 23:57:42.471][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 23:57:42.474][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-13 23:57:42.477][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-13 23:57:42.479][biodb::testThat]
biodb.INFO [2025-03-13 23:57:42.480][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-03-13 23:57:42.481][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:57:42.486][biodb::testThat]
biodb.DEBUG[2025-03-13 23:57:42.492][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-13 23:57:42.498][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:42.500][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-13 23:57:42.503][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:42.505][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-13 23:57:42.512][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-13 23:57:42.520][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:42.522][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:42.525][private$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[2025-03-13 23:57:42.933][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[2025-03-13 23:57:43.348][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:43.353][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-03-13 23:57:43.359][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-03-13 23:57:43.374][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-13 23:57:43.376][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-13 23:57:43.379][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-13 23:57:43.380][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-13 23:57:43.382][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:43.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:43.384][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:43.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:43.387][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:43.388][FUN] Functions in observer BiodbConfig: [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 [2025-03-13 23:57:43.397][biodb::testContext]
biodb.INFO [2025-03-13 23:57:43.399][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-13 23:57:43.401][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-03-13 23:57:43.404][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-13 23:57:43.405][biodb::testContext]
biodb.INFO [2025-03-13 23:57:43.408][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-13 23:57:43.410][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-13 23:57:43.418][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 23:57:43.420][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-13 23:57:43.423][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-13 23:57:43.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:43.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:43.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:43.434][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-13 23:57:43.437][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-13 23:57:43.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:43.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:43.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:43.446][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-13 23:57:43.449][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-13 23:57:43.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:43.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:43.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:43.459][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-13 23:57:43.460][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-13 23:57:43.463][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-13 23:57:43.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:43.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:43.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:43.471][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-13 23:57:43.474][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-13 23:57:43.476][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-13 23:57:43.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:43.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:43.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:43.485][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-13 23:57:43.487][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-13 23:57:43.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:43.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:43.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:43.497][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-13 23:57:43.499][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-13 23:57:43.502][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-13 23:57:43.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:43.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:43.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:43.510][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-13 23:57:43.513][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-13 23:57:43.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:43.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:43.532][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[2025-03-13 23:57:43.535][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-13 23:57:43.537][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-13 23:57:43.540][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-13 23:57:43.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:43.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:43.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:43.551][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-13 23:57:43.556][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-13 23:57:43.558][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-13 23:57:43.561][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-13 23:57:43.563][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-13 23:57:43.577][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-13 23:57:43.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:43.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:43.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:43.588][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-13 23:57:43.590][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-13 23:57:43.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:43.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:43.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:43.595][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-13 23:57:43.598][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-13 23:57:43.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:43.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:43.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:43.605][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-13 23:57:43.608][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-13 23:57:43.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:43.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:43.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:43.614][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-13 23:57:43.617][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-13 23:57:43.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:43.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:43.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:43.624][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-13 23:57:43.626][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-13 23:57:43.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:43.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:43.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:43.632][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-13 23:57:43.634][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-13 23:57:43.791][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-13 23:57:43.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:43.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:43.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:43.799][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-13 23:57:43.800][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-13 23:57:43.803][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-13 23:57:43.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:43.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:43.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:43.812][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-13 23:57:43.814][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:43.816][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-13 23:57:43.817][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:43.822][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:57:43.825][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:43.827][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:57:43.830][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:43.836][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 23:57:43.839][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-13 23:57:43.841][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:57:43.843][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:43.848][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-13 23:57:43.850][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:57:43.851][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:43.853][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:43.854][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 23:57:43.854][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-13 23:57:43.854][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-13 23:57:43.854][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-13 23:57:43.854][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-13 23:57:43.855][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 23:57:43.857][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:43.858][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:43.863][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:57:43.865][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:43.866][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:43.868][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:57:43.869][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:43.870][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:57:43.872][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:57:43.875][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:43.878][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:43.881][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-13 23:57:43.885][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:43.887][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-13 23:57:43.890][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:43.892][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:57:43.895][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:43.898][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:57:43.900][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:43.903][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 23:57:43.904][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-13 23:57:43.909][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:57:43.912][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:43.914][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-13 23:57:43.917][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:57:43.940][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:43.943][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:43.951][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 23:57:43.951][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-13 23:57:43.951][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-13 23:57:43.951][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-13 23:57:43.951][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-13 23:57:43.954][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 23:57:43.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:43.967][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:43.969][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:57:43.972][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:43.974][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:43.978][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:57:43.981][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:43.983][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:57:43.985][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:57:43.987][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:43.990][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:43.994][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-13 23:57:43.997][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:43.999][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-13 23:57:44.000][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:44.003][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:57:44.005][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:44.007][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:57:44.009][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:44.010][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 23:57:44.012][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-13 23:57:44.013][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:57:44.014][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:44.016][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-13 23:57:44.022][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:57:44.026][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:44.032][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:44.038][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:44.043][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 23:57:44.089][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:44.091][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:44.094][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:57:44.108][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:44.110][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:44.113][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:57:44.118][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:44.122][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:57:44.124][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:57:44.127][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:44.129][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:44.136][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-13 23:57:44.142][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:44.148][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-13 23:57:44.151][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:44.153][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:57:44.155][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:44.160][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:57:44.163][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:44.165][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-13 23:57:44.168][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-13 23:57:44.174][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:57:44.177][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:44.179][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-13 23:57:44.182][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:57:44.187][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:44.189][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:44.192][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:44.194][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-13 23:57:44.199][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:44.201][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:44.203][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:57:44.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:44.207][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:44.210][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:57:44.212][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:44.214][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:57:44.216][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:57:44.218][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:44.220][self$setPropertyValue]
biodb.DEBUG[2025-03-13 23:57:44.221][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 23:57:44.223][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.285][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.DEBUG[2025-03-13 23:57:44.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.415][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[2025-03-13 23:57:44.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.461][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-13 23:57:44.464][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-13 23:57:44.467][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-13 23:57:44.477][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-13 23:57:44.481][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-13 23:57:44.485][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-13 23:57:44.489][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-13 23:57:44.497][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-13 23:57:44.504][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-13 23:57:44.507][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-13 23:57:44.514][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-13 23:57:44.517][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-13 23:57:44.520][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-13 23:57:44.524][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-13 23:57:44.528][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-13 23:57:44.531][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-13 23:57:44.536][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-13 23:57:44.539][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-13 23:57:44.542][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-13 23:57:44.547][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-13 23:57:44.551][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-13 23:57:44.555][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-13 23:57:44.560][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-13 23:57:44.564][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-13 23:57:44.568][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-13 23:57:44.571][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-13 23:57:44.576][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-13 23:57:44.579][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-13 23:57:44.582][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-13 23:57:44.586][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-13 23:57:44.590][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-13 23:57:44.595][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-13 23:57:44.599][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-13 23:57:44.602][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-13 23:57:44.606][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-13 23:57:44.610][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-13 23:57:44.613][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-13 23:57:44.616][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-13 23:57:44.620][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-13 23:57:44.623][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-13 23:57:44.626][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-13 23:57:44.630][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-13 23:57:44.633][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-13 23:57:44.636][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-13 23:57:44.643][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-13 23:57:44.647][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-13 23:57:44.650][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-13 23:57:44.653][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-13 23:57:44.657][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-13 23:57:44.660][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-13 23:57:44.664][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-13 23:57:44.667][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-13 23:57:44.671][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-13 23:57:44.675][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-13 23:57:44.679][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-13 23:57:44.682][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-13 23:57:44.686][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-13 23:57:44.693][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-13 23:57:44.697][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-13 23:57:44.700][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-13 23:57:44.703][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-13 23:57:44.707][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-13 23:57:44.709][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-13 23:57:44.712][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-13 23:57:44.715][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-13 23:57:44.719][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-13 23:57:44.725][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-13 23:57:44.728][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-13 23:57:44.731][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-13 23:57:44.735][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-13 23:57:44.738][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-13 23:57:44.741][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-13 23:57:44.744][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-13 23:57:44.748][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-13 23:57:44.751][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-13 23:57:44.754][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-13 23:57:44.760][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-13 23:57:44.764][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-13 23:57:44.767][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-13 23:57:44.771][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-13 23:57:44.774][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-13 23:57:44.777][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-13 23:57:44.782][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-13 23:57:44.785][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-13 23:57:44.790][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-13 23:57:44.793][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-13 23:57:44.795][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.799][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:44.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:44.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.819][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[2025-03-13 23:57:44.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:44.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:44.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:44.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:44.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:44.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:44.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:44.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:44.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.894][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[2025-03-13 23:57:44.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:44.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:44.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:44.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:44.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:44.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:44.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:44.965][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[2025-03-13 23:57:44.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:44.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:44.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:44.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:44.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:45.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:45.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:45.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:45.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:45.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:45.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:45.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:45.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:45.051][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[2025-03-13 23:57:45.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:45.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:45.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:45.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:45.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:45.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:45.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:45.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:45.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:45.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:45.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:45.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:45.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:45.085][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[2025-03-13 23:57:45.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:45.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:45.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:45.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:45.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:45.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:45.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:45.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:45.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:45.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:45.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:45.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:45.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:45.130][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[2025-03-13 23:57:45.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:45.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:45.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:45.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:45.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:45.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:45.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:45.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:45.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:45.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:45.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:45.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:45.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:45.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:45.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:45.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:45.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:45.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:45.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:45.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:45.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:45.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-13 23:57:45.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:45.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:45.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:45.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:45.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:45.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-13 23:57:45.193][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-13 23:57:45.198][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-13 23:57:45.202][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:45.204][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-13 23:57:45.206][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:45.209][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-13 23:57:45.213][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:45.215][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-13 23:57:45.217][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:45.220][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-13 23:57:45.222][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-13 23:57:45.224][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-13 23:57:45.226][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:45.229][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-13 23:57:45.232][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-13 23:57:45.234][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-13 23:57:45.234][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-13 23:57:45.234][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-13 23:57:45.234][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-13 23:57:45.234][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-13 23:57:45.234][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-13 23:57:45.234][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-13 23:57:45.234][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-13 23:57:45.234][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-13 23:57:45.234][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-13 23:57:45.234][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-13 23:57:45.236][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-13 23:57:45.238][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-13 23:57:45.238][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-13 23:57:45.238][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-13 23:57:45.239][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-13 23:57:45.242][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:45.244][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:45.246][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-13 23:57:45.248][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-13 23:57:45.249][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-13 23:57:45.252][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-13 23:57:45.254][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:57:45.254][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-13 23:57:45.256][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-13 23:57:45.258][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-13 23:57:45.263][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-13 23:57:45.264][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-13 23:57:45.264][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-13 23:57:45.266][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-13 23:57:45.268][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-13 23:57:45.276][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-13 23:57:45.279][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-13 23:57:45.282][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-13 23:57:45.284][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-13 23:57:45.290][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-13 23:57:45.292][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-13 23:57:45.295][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-13 23:57:45.305][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-13 23:57:45.307][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 23:57:45.308][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-13 23:57:45.310][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-13 23:57:45.312][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-13 23:57:45.313][biodb::testThat]
biodb.INFO [2025-03-13 23:57:45.315][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-03-13 23:57:45.328][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-13 23:57:45.330][biodb::testThat]
biodb.DEBUG[2025-03-13 23:57:45.341][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-13 23:57:45.367][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:45.370][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-13 23:57:45.374][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:45.413][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-13 23:57:45.422][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[2025-03-13 23:57:45.450][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-13 23:57:45.453][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-03-13 23:57:45.456][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-13 23:57:45.459][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-03-13 23:57:45.468][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-03-13 23:57:45.497][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-13 23:57:45.501][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-03-13 23:57:45.503][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-13 23:57:45.513][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-13 23:57:45.515][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-13 23:57:45.518][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-13 23:57:45.530][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-13 23:57:45.533][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-13 23:57:45.541][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:45.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:45.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:45.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:45.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:45.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:45.593][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.DEBUG[2025-03-13 23:57:45.597][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-03-13 23:57:45.604][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-13 23:57:45.620][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-13 23:57:45.622][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-03-13 23:57:46.074][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-03-13 23:57:46.767][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-13 23:57:46.772][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-03-13 23:57:46.783][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-03-13 23:57:46.789][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-03-13 23:57:46.794][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-13 23:57:46.798][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-13 23:57:46.801][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-13 23:57:46.805][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-13 23:57:46.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:46.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:46.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:46.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:46.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:46.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-13 23:57:46.839][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:46.842][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:46.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:46.847][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:46.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:46.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:46.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:46.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:46.862][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:46.865][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:46.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:46.870][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:46.873][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-13 23:57:46.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-13 23:57:46.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:46.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:46.884][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:46.887][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:46.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:46.892][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:46.895][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-13 23:57:46.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-13 23:57:46.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:46.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:46.909][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-13 23:57:46.912][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-13 23:57:46.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:46.926][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:46.930][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-13 23:57:46.932][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-13 23:57:46.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:46.948][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:46.952][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:46.955][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:46.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:46.971][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:46.975][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:46.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-13 23:57:46.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:46.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.010][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:47.013][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:47.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.029][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.033][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-13 23:57:47.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-13 23:57:47.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.054][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:47.056][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:47.065][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.067][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:47.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-13 23:57:47.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.091][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:47.104][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:47.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.109][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.123][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-13 23:57:47.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-13 23:57:47.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.143][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:47.146][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:47.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.151][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.163][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-13 23:57:47.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-13 23:57:47.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.182][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:47.185][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:47.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.190][ef$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.204][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-13 23:57:47.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-13 23:57:47.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:47.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:47.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.242][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:47.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:47.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:47.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:47.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-13 23:57:47.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-13 23:57:47.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:47.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:47.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:47.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:47.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:47.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:47.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:47.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:47.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:47.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:47.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-13 23:57:47.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-13 23:57:47.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-13 23:57:47.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-13 23:57:47.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-13 23:57:47.381][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-03-13 23:57:47.392][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-13 23:57:47.395][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-13 23:57:47.396][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-13 23:57:47.400][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-13 23:57:47.402][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-13 23:57:47.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-13 23:57:47.405][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-13 23:57:47.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-13 23:57:47.408][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-13 23:57:47.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 385 ]
> 
> proc.time()
   user  system elapsed 
 38.586   2.110 107.099

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn4.6691.2556.875
ChebiEntry0.8180.0241.618