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This page was generated on 2025-02-11 11:43 -0500 (Tue, 11 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4719
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4480
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4491
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4444
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 202/2295HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.13.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-02-10 13:40 -0500 (Mon, 10 Feb 2025)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: devel
git_last_commit: 686a27c
git_last_commit_date: 2024-10-29 11:04:36 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for biodbChebi on kjohnson3

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

raw results


Summary

Package: biodbChebi
Version: 1.13.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.13.0.tar.gz
StartedAt: 2025-02-10 18:16:25 -0500 (Mon, 10 Feb 2025)
EndedAt: 2025-02-10 18:17:35 -0500 (Mon, 10 Feb 2025)
EllapsedTime: 70.8 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbChebi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘biodbChebi’ ...
** this is package ‘biodbChebi’ version ‘1.13.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbChebi)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-02-10 18:16:45.556][biodb::testContext]
biodb.INFO [2025-02-10 18:16:45.558][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-10 18:16:45.558][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-02-10 18:16:45.558][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-10 18:16:45.559][biodb::testContext]
biodb.INFO [2025-02-10 18:16:45.561][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-10 18:16:45.562][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-10 18:16:45.565][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 18:16:45.566][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-10 18:16:45.566][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-10 18:16:45.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.567][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-10 18:16:45.574][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-10 18:16:45.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.576][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[2025-02-10 18:16:45.576][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-10 18:16:45.576][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-10 18:16:45.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.578][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-10 18:16:45.578][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-10 18:16:45.578][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-10 18:16:45.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.579][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-10 18:16:45.580][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-10 18:16:45.580][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-10 18:16:45.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.581][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-10 18:16:45.581][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-10 18:16:45.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.582][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-10 18:16:45.583][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-10 18:16:45.583][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-10 18:16:45.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.584][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-10 18:16:45.591][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-10 18:16:45.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.593][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-10 18:16:45.593][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-10 18:16:45.593][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-10 18:16:45.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.594][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-10 18:16:45.594][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-10 18:16:45.595][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-10 18:16:45.595][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-10 18:16:45.595][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-10 18:16:45.595][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-10 18:16:45.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.596][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-10 18:16:45.597][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-10 18:16:45.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.598][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-10 18:16:45.598][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-10 18:16:45.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.599][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-10 18:16:45.599][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-10 18:16:45.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.600][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-10 18:16:45.600][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-10 18:16:45.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.601][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-10 18:16:45.601][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-10 18:16:45.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.602][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-10 18:16:45.603][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-10 18:16:45.610][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-10 18:16:45.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.610][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[2025-02-10 18:16:45.611][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-10 18:16:45.611][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-10 18:16:45.611][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-10 18:16:45.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.614][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-10 18:16:45.625][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:16:45.630][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-10 18:16:45.630][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.630][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:16:45.631][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.631][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:16:45.631][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 18:16:45.632][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 18:16:45.632][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-10 18:16:45.632][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:16:45.632][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.633][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-10 18:16:45.633][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:16:45.633][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:16:45.633][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.634][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 18:16:45.634][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 18:16:45.634][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 18:16:45.634][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-10 18:16:45.634][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-10 18:16:45.634][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 18:16:45.634][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:16:45.635][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:16:45.635][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:16:45.635][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:16:45.635][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:16:45.636][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:16:45.636][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:16:45.636][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:16:45.636][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:16:45.637][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 18:16:45.637][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:16:45.637][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-10 18:16:45.638][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:16:45.638][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-10 18:16:45.638][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.638][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:16:45.639][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.639][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:16:45.639][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 18:16:45.639][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 18:16:45.640][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-10 18:16:45.640][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:16:45.640][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.641][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-10 18:16:45.641][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:16:45.641][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:16:45.641][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.642][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 18:16:45.642][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 18:16:45.642][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 18:16:45.642][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-10 18:16:45.642][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-10 18:16:45.642][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 18:16:45.642][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:16:45.642][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:16:45.643][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:16:45.643][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:16:45.643][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:16:45.643][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:16:45.644][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:16:45.644][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:16:45.644][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:16:45.644][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 18:16:45.645][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:16:45.645][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-10 18:16:45.645][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.646][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-10 18:16:45.646][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.646][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:16:45.647][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.647][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:16:45.647][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 18:16:45.647][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 18:16:45.648][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-10 18:16:45.648][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:16:45.648][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:16:45.648][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-10 18:16:45.649][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:16:45.649][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:16:45.649][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.649][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:16:45.650][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 18:16:45.650][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:16:45.650][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:16:45.650][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:16:45.651][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:16:45.651][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:16:45.651][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:16:45.651][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:16:45.651][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:16:45.652][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:16:45.652][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 18:16:45.652][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:16:45.653][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-10 18:16:45.653][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.653][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-10 18:16:45.654][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.654][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:16:45.654][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.654][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:16:45.655][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 18:16:45.655][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 18:16:45.655][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-10 18:16:45.655][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:16:45.656][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:16:45.656][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-10 18:16:45.656][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:16:45.657][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:16:45.659][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.660][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:16:45.660][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 18:16:45.660][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:16:45.660][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:16:45.661][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:16:45.661][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:16:45.661][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:16:45.661][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:16:45.662][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:16:45.662][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:16:45.662][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:16:45.662][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 18:16:45.663][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:16:45.664][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 18:16:45.664][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.668][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[2025-02-10 18:16:45.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.678][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.DEBUG[2025-02-10 18:16:45.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.684][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-10 18:16:45.685][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-10 18:16:45.686][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-10 18:16:45.686][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-10 18:16:45.686][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-10 18:16:45.687][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-10 18:16:45.687][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-10 18:16:45.687][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-10 18:16:45.688][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-10 18:16:45.688][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-10 18:16:45.689][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-10 18:16:45.689][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-10 18:16:45.689][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-10 18:16:45.690][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-10 18:16:45.690][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-10 18:16:45.690][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-10 18:16:45.691][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-10 18:16:45.691][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-10 18:16:45.691][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-10 18:16:45.692][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-10 18:16:45.692][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-10 18:16:45.692][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-10 18:16:45.693][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-10 18:16:45.693][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-10 18:16:45.694][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-10 18:16:45.694][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-10 18:16:45.694][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-10 18:16:45.695][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-10 18:16:45.695][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-10 18:16:45.695][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-10 18:16:45.696][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-10 18:16:45.696][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-10 18:16:45.696][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-10 18:16:45.697][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-10 18:16:45.697][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-10 18:16:45.697][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-10 18:16:45.698][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-10 18:16:45.698][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-10 18:16:45.698][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-10 18:16:45.699][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-10 18:16:45.699][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-10 18:16:45.700][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-10 18:16:45.700][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-10 18:16:45.700][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-10 18:16:45.701][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-10 18:16:45.701][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-10 18:16:45.701][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-10 18:16:45.702][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-10 18:16:45.702][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-10 18:16:45.702][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-10 18:16:45.703][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-10 18:16:45.703][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-10 18:16:45.703][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-10 18:16:45.704][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-10 18:16:45.704][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-10 18:16:45.705][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-10 18:16:45.705][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-10 18:16:45.705][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-10 18:16:45.706][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-10 18:16:45.706][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-10 18:16:45.706][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-10 18:16:45.707][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-10 18:16:45.707][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-10 18:16:45.707][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-10 18:16:45.708][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-10 18:16:45.708][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-10 18:16:45.708][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-10 18:16:45.709][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-10 18:16:45.709][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-10 18:16:45.709][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-10 18:16:45.710][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-10 18:16:45.710][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-10 18:16:45.710][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-10 18:16:45.711][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-10 18:16:45.711][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-10 18:16:45.711][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-10 18:16:45.712][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-10 18:16:45.712][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-10 18:16:45.715][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-10 18:16:45.715][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-10 18:16:45.716][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-10 18:16:45.716][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-10 18:16:45.717][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-10 18:16:45.718][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-10 18:16:45.719][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-10 18:16:45.720][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 18:16:45.720][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.721][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.721][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[2025-02-10 18:16:45.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:45.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:45.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:45.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:45.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:45.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:45.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.727][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.DEBUG[2025-02-10 18:16:45.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:45.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:45.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:45.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:45.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:45.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:45.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:45.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:45.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:45.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:45.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:45.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:45.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:45.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:45.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:45.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:45.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:45.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:45.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:45.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:45.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:45.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:45.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:45.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:45.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:45.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:45.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:16:45.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:45.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:45.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:45.749][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-02-10 18:16:45.753][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-02-10 18:16:45.753][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:16:45.753][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-10 18:16:45.754][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.754][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:16:45.754][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.754][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:16:45.755][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.755][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-02-10 18:16:45.755][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-10 18:16:45.755][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:16:45.756][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.756][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-02-10 18:16:45.756][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:16:45.757][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-02-10 18:16:45.757][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-02-10 18:16:45.757][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-02-10 18:16:45.757][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-02-10 18:16:45.757][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-02-10 18:16:45.757][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-02-10 18:16:45.757][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-02-10 18:16:45.757][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-02-10 18:16:45.757][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-02-10 18:16:45.757][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-02-10 18:16:45.757][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-02-10 18:16:45.757][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-10 18:16:45.757][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 18:16:45.757][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 18:16:45.757][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 18:16:45.757][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-10 18:16:45.758][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:16:45.758][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:16:45.758][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:16:45.758][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:16:45.759][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:16:45.759][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:16:45.759][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:16:45.759][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-02-10 18:16:45.759][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:16:45.760][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:16:45.760][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-10 18:16:45.760][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-02-10 18:16:45.760][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-02-10 18:16:45.762][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-10 18:16:45.762][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-10 18:16:45.763][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-02-10 18:16:45.763][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-10 18:16:45.764][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-10 18:16:45.764][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-10 18:16:45.774][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-02-10 18:16:45.774][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-02-10 18:16:45.778][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-02-10 18:16:45.780][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-02-10 18:16:45.782][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-10 18:16:45.782][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-10 18:16:45.782][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-02-10 18:16:45.783][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-02-10 18:16:45.786][biodb::testThat]
biodb.INFO [2025-02-10 18:16:45.787][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-02-10 18:16:45.787][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:16:45.787][biodb::testThat]
biodb.TRACE[2025-02-10 18:16:45.789][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-02-10 18:16:45.790][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:45.791][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:45.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:45.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:45.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:45.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:45.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:45.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:45.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:45.805][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.805][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.806][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.811][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:45.812][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:45.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.812][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.820][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:45.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:45.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.822][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:45.822][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:45.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.823][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.823][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:45.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:45.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.824][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:45.824][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:45.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.825][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.825][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:45.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:45.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.826][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:45.827][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:45.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.827][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.827][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:45.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:45.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.829][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:45.829][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:45.829][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.829][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.830][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:45.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:45.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.831][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:45.831][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:45.831][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.831][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.832][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:45.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:45.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.833][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:45.833][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:45.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.834][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:45.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:45.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.835][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:45.835][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:45.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.836][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.836][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:45.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:45.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.837][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:45.837][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:45.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.838][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.839][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:45.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:45.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.840][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:45.840][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:45.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.841][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.841][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:45.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:45.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:45.878][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-02-10 18:16:45.878][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:45.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:45.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.880][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:45.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:45.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.888][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:45.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:45.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.889][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:45.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:45.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:45.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:45.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:45.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:45.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.892][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-10 18:16:45.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-10 18:16:45.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.893][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-10 18:16:45.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-10 18:16:45.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.894][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-10 18:16:45.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-10 18:16:45.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.895][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-10 18:16:45.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-10 18:16:45.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.930][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.930][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.930][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.931][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:45.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:45.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.936][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.938][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.939][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.939][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:45.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.943][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:45.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:45.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.944][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:45.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:45.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:45.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:45.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.946][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:45.947][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:45.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.947][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.947][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:45.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:45.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.951][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:45.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:45.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.952][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:45.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:45.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.953][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:45.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:45.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.954][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:45.954][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:45.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.955][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.955][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:45.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:45.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:45.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:45.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:45.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:45.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.964][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:45.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:45.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.965][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:45.965][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:45.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.965][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.966][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:45.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:45.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:45.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:45.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:45.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:45.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:45.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:45.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.972][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:45.973][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:45.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.973][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:45.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:45.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.977][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:45.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:45.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.978][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:45.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:45.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.979][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:45.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:45.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.980][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:45.980][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:45.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.981][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.981][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:45.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:45.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.984][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-10 18:16:45.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:45.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.985][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-10 18:16:45.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:45.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.986][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-10 18:16:45.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:45.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.987][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-10 18:16:45.988][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:45.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.988][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.988][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-10 18:16:45.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:45.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.992][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:45.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:45.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.993][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:45.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:45.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.994][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:45.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:45.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.995][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:45.995][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:45.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.996][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:45.996][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:45.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:45.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:45.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.000][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:46.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:46.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.001][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:46.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:46.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.002][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:46.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:46.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.003][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:46.003][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:46.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.004][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.004][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:46.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:46.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.008][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.009][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.010][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.011][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.011][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.014][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.014][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.018][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:46.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:46.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:46.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:46.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.020][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:46.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:46.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.021][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:46.022][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:46.022][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.022][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.022][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:46.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:46.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.026][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:46.026][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:46.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.027][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.028][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:46.029][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:46.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.029][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.030][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:46.031][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:46.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.031][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.033][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:46.033][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:46.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.034][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.035][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.035][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.036][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.037][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:46.038][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:46.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.038][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.040][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:46.040][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:46.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.040][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.042][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:46.042][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:46.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.043][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.044][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-10 18:16:46.044][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:46.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.045][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.046][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:46.047][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:46.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.047][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.049][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:46.049][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:46.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.049][ef$get] fields variable is a list.
biodb.INFO [2025-02-10 18:16:46.052][biodb::testThat]
biodb.INFO [2025-02-10 18:16:46.052][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-02-10 18:16:46.052][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:16:46.053][biodb::testThat]
biodb.DEBUG[2025-02-10 18:16:46.057][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-02-10 18:16:46.060][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:46.061][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-02-10 18:16:46.061][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:46.062][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-02-10 18:16:46.062][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:46.073][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:46.073][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:46.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:46.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:46.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:46.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:46.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:46.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:46.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:46.078][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:46.078][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:46.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.078][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:46.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:46.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.085][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:46.085][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:46.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.086][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.086][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:46.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:46.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.087][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:46.087][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:46.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.088][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.088][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:46.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:46.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.089][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:46.090][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:46.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.090][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.090][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:46.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:46.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.091][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.092][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.092][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.092][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.093][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:46.094][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:46.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.094][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.094][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:46.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:46.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.095][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:46.096][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:46.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.096][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.096][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:46.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:46.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.098][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:46.098][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:46.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.098][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:46.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:46.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.100][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:46.100][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:46.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.100][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.101][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:46.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:46.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.102][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:46.102][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:46.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.102][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.103][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:46.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:46.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.104][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:46.104][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:46.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.105][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.105][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:46.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:46.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:46.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:46.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:46.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:46.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:46.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:46.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:46.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:46.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:46.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:46.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:46.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:46.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:46.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:46.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:46.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:46.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:46.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:46.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:46.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:46.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:46.118][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-02-10 18:16:46.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-02-10 18:16:46.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-02-10 18:16:46.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.119][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-02-10 18:16:46.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-02-10 18:16:46.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.120][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-02-10 18:16:46.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-02-10 18:16:46.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-10 18:16:46.124][biodb::testThat]
biodb.INFO [2025-02-10 18:16:46.124][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-02-10 18:16:46.125][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:16:46.125][biodb::testThat]
biodb.TRACE[2025-02-10 18:16:46.126][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:46.126][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:46.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.127][ef$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:46.127][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-02-10 18:16:46.136][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:46.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:46.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:46.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:46.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:46.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:46.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:46.140][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-02-10 18:16:46.142][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-02-10 18:16:46.148][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:16:46.153][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-02-10 18:16:46.153][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:46.154][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-02-10 18:16:46.161][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:16:46.162][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:16:46.162][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-10 18:16:46.167][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:46.168][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-02-10 18:16:46.169][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-02-10 18:16:46.173][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:46.173][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:46.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.174][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.174][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:46.174][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:46.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.175][ef$get] fields variable is a list.
biodb.INFO [2025-02-10 18:16:46.177][biodb::testThat]
biodb.INFO [2025-02-10 18:16:46.177][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-02-10 18:16:46.178][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:16:46.178][biodb::testThat]
biodb.TRACE[2025-02-10 18:16:46.186][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:46.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:46.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.188][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:46.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:46.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.189][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:46.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:46.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:46.208][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:16:46.209][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:16:46.210][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-10 18:16:46.210][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:46.211][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-02-10 18:16:46.217][biodb::testThat]
biodb.INFO [2025-02-10 18:16:46.217][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-02-10 18:16:46.218][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:16:46.218][biodb::testThat]
biodb.TRACE[2025-02-10 18:16:46.227][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:46.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:46.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.228][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:46.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:46.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.229][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:46.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:46.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:46.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:46.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.234][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-10 18:16:46.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-10 18:16:46.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.235][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-10 18:16:46.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-10 18:16:46.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.236][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-10 18:16:46.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-10 18:16:46.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.237][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-10 18:16:46.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-10 18:16:46.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.243][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:46.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:46.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.244][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:46.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:46.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.246][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:46.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:46.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:46.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:46.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:46.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.250][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-10 18:16:46.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-10 18:16:46.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.251][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-10 18:16:46.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-10 18:16:46.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.252][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-10 18:16:46.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-10 18:16:46.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:46.253][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-10 18:16:46.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-10 18:16:46.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:46.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-10 18:16:46.257][biodb::testThat]
biodb.INFO [2025-02-10 18:16:46.257][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-02-10 18:16:46.257][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:16:46.257][biodb::testThat]
biodb.INFO [2025-02-10 18:16:46.260][biodb::testThat]
biodb.INFO [2025-02-10 18:16:46.261][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-02-10 18:16:46.261][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:16:46.261][biodb::testThat]
biodb.INFO [2025-02-10 18:16:46.264][biodb::testThat]
biodb.INFO [2025-02-10 18:16:46.264][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-02-10 18:16:46.265][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:16:46.265][biodb::testThat]
biodb.DEBUG[2025-02-10 18:16:46.266][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-02-10 18:16:47.254][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-02-10 18:16:48.672][biodb::testThat]
biodb.INFO [2025-02-10 18:16:48.672][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-02-10 18:16:48.672][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:16:48.673][biodb::testThat]
biodb.DEBUG[2025-02-10 18:16:49.088][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2025-02-10 18:16:49.498][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:49.498][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:49.498][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.498][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.499][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.499][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.499][ef$get] fields variable is a list.
biodb.INFO [2025-02-10 18:16:49.500][biodb::testThat]
biodb.INFO [2025-02-10 18:16:49.500][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-02-10 18:16:49.501][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:16:49.501][biodb::testThat]
biodb.TRACE[2025-02-10 18:16:49.505][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:49.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:49.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:49.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:49.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.507][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:49.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:49.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:49.537][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:16:49.538][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:16:49.538][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-10 18:16:49.539][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:49.539][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-02-10 18:16:49.561][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:16:49.562][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:16:49.563][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-10 18:16:49.563][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:49.564][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-02-10 18:16:49.568][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-10 18:16:49.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-10 18:16:49.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:49.578][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:16:49.580][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:16:49.580][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-02-10 18:16:49.580][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:49.581][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-02-10 18:16:49.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:49.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:49.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:49.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:49.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:49.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:49.584][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[2025-02-10 18:16:49.585][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-02-10 18:16:49.601][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:49.601][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-02-10 18:16:49.602][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:49.602][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml".
biodb.DEBUG[2025-02-10 18:16:49.603][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:49.603][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:49.603][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:49.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:49.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:49.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:49.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:49.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:49.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:49.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:49.607][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.608][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.608][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.610][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:49.610][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:49.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.610][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.611][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:49.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:49.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.612][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:49.612][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:49.612][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.613][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.613][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:49.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:49.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.614][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:49.614][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:49.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.615][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.615][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:49.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:49.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.616][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.616][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.617][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.617][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.618][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.619][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.619][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.619][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:49.620][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.620][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.620][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:49.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.621][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.622][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.622][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.623][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:49.624][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:49.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.624][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.624][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:49.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:49.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.625][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:49.626][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:49.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.626][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.627][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:49.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:49.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.628][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:49.628][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:49.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.628][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.629][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:49.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:49.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:49.641][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-02-10 18:16:49.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:49.647][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:16:49.648][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:16:49.648][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-02-10 18:16:49.649][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:49.649][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-02-10 18:16:49.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:49.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:49.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:49.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:49.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:49.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:49.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:49.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:49.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:49.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:49.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:49.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:49.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:49.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:49.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:49.664][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-02-10 18:16:49.664][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:49.665][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-02-10 18:16:49.665][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:49.668][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml".
biodb.DEBUG[2025-02-10 18:16:49.669][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:49.669][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:49.670][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:49.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:49.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:49.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:49.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:49.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:49.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:49.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:49.674][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.675][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.675][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.677][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:49.677][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:49.677][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.677][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.678][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:49.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:49.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.679][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:49.679][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:49.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.679][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.680][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:49.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:49.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.681][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:49.681][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:49.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.682][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.682][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:49.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:49.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.683][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.683][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.684][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.684][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.685][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.685][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.686][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.686][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:49.686][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.687][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.687][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:49.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.688][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.688][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.689][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.690][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:49.690][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:49.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.691][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:49.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:49.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.692][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:49.693][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:49.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.693][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.693][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:49.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:49.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.694][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:49.695][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:49.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.695][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.695][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:49.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:49.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:49.709][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-02-10 18:16:49.709][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:49.718][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:16:49.719][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:16:49.720][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-10 18:16:49.720][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:49.721][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-02-10 18:16:49.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:49.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:49.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:49.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:49.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:49.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:49.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:49.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:49.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:49.728][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:49.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:49.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:49.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:49.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:49.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:49.731][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-02-10 18:16:49.731][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:49.731][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-02-10 18:16:49.732][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:49.732][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml".
biodb.DEBUG[2025-02-10 18:16:49.733][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:49.733][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:49.734][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:49.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:49.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:49.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:49.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:49.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:49.737][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:49.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:49.738][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.738][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.738][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.740][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:49.740][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:49.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.741][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.741][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:49.741][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:49.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.742][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.742][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:49.742][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:49.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.745][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.745][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.746][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.746][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.746][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.747][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.747][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.747][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.748][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:49.748][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.748][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.749][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.749][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.749][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.750][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:49.750][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:49.750][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.750][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.751][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:49.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:49.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.752][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:49.752][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:49.752][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.753][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.753][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:49.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:49.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.755][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:49.755][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:49.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.755][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:49.766][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-02-10 18:16:49.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.769][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:49.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:49.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:49.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:49.773][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:49.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:49.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:49.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:49.775][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-02-10 18:16:49.775][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:49.775][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-02-10 18:16:49.776][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:49.777][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml".
biodb.DEBUG[2025-02-10 18:16:49.777][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:49.778][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:49.778][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:49.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:49.779][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:49.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:49.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:49.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:49.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:49.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:49.785][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.785][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.786][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.787][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:49.787][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:49.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.788][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.788][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:49.788][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:49.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.789][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.789][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:49.790][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:49.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.790][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.790][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.791][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.791][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.791][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.792][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.792][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.792][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:49.793][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.793][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.793][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.794][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.794][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.795][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:49.795][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:49.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.795][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:49.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:49.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.797][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:49.797][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:49.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.798][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.798][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:49.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:49.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.799][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:49.800][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:49.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.800][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:49.811][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-02-10 18:16:49.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:49.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:49.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:49.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:49.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:49.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:49.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:49.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:49.822][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-02-10 18:16:49.822][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:49.823][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-02-10 18:16:49.823][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:49.824][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml".
biodb.DEBUG[2025-02-10 18:16:49.824][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:49.825][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:49.825][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:49.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:49.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:49.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:49.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:49.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:49.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:49.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:49.829][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.829][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.830][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.831][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:49.832][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:49.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.832][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.833][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:49.833][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:49.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.833][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.834][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:49.834][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:49.834][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.834][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.835][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.835][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.835][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.836][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.836][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.836][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.837][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:49.837][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.837][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.838][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.838][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.839][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.839][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:49.839][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:49.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.840][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:49.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:49.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.841][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:49.841][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:49.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.842][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.842][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:49.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:49.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.843][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:49.844][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:49.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.844][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:49.857][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-02-10 18:16:49.858][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.861][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:49.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:49.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:49.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:49.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:49.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:49.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:49.866][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[2025-02-10 18:16:49.866][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-02-10 18:16:49.867][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:49.867][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-02-10 18:16:49.867][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:49.868][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml".
biodb.DEBUG[2025-02-10 18:16:49.868][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:49.869][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:49.869][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:49.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:49.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:49.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:49.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:49.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:49.872][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:49.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:49.873][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.874][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.874][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.874][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.876][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:49.876][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:49.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.876][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.877][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:49.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:49.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.878][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:49.878][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:49.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.879][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.879][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:49.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:49.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.880][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:49.880][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:49.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.881][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.881][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:49.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:49.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.882][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.882][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.883][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.883][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.883][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.884][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.884][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.885][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.885][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.886][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:49.886][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.887][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.887][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:49.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.888][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.889][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.889][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.890][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:49.891][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:49.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.891][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.892][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:49.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:49.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.896][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:49.896][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:49.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.896][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.897][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:49.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:49.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.898][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:49.898][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:49.898][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.899][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.899][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:49.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:49.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:49.911][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-02-10 18:16:49.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:49.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:49.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:49.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:49.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:49.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:49.917][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:49.917][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[2025-02-10 18:16:49.917][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-02-10 18:16:49.917][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:49.918][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-02-10 18:16:49.919][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:49.919][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml".
biodb.DEBUG[2025-02-10 18:16:49.919][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:49.920][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:49.920][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:49.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:49.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:49.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:49.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:49.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:49.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:49.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:49.924][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.925][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.925][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.927][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:49.927][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:49.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.927][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.928][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:49.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:49.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.929][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:49.929][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:49.929][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.929][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.930][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:49.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:49.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.933][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:49.934][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:49.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.934][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.935][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:49.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:49.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.936][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.936][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.937][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.937][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.938][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.938][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.939][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.939][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.940][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:49.940][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.941][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.941][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:49.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.942][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.942][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.943][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:49.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.944][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:49.944][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:49.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.945][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:49.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:49.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.946][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:49.946][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:49.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.947][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.947][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:49.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:49.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.948][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:49.948][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:49.949][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.949][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.949][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:49.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:49.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.950][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:49.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:49.960][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-02-10 18:16:49.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:49.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:49.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:49.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:49.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:49.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:49.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:49.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:49.980][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[2025-02-10 18:16:49.981][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-02-10 18:16:49.981][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:49.982][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-02-10 18:16:49.982][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:49.983][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml".
biodb.DEBUG[2025-02-10 18:16:49.983][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:49.983][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:49.984][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:49.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:49.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:49.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:49.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:49.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:49.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:49.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:49.988][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.988][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.989][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:49.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:49.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.990][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:49.990][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:49.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.991][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.991][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:49.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:49.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.992][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:49.992][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:49.993][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.993][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.993][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:49.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:49.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.994][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:49.995][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:49.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.995][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.995][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:49.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:49.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.996][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.997][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.997][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.997][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:49.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:49.998][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.999][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:49.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:49.999][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.000][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:50.000][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.000][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.000][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.001][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:50.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.002][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.002][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.002][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.004][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:50.004][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:50.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.005][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.005][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:50.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:50.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.006][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:50.006][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:50.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.007][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.007][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:50.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:50.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.008][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:50.008][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:50.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.009][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.009][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:50.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:50.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:50.024][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-02-10 18:16:50.024][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:50.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:50.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:50.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:50.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:50.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:50.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:50.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:50.031][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-02-10 18:16:50.031][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:50.031][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-02-10 18:16:50.032][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:50.032][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml".
biodb.DEBUG[2025-02-10 18:16:50.033][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:50.033][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:50.033][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:50.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:50.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:50.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:50.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:50.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:50.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:50.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:50.037][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.038][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.038][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.040][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:50.040][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:50.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.040][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.041][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:50.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:50.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.042][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:50.042][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:50.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.042][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.043][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:50.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:50.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.044][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:50.044][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:50.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.044][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.045][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:50.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:50.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.046][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:50.046][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:50.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.047][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.047][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:50.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:50.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.048][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:50.048][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:50.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.049][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.049][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:50.049][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.050][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.050][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:50.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.051][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.051][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.052][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.056][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:50.056][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:50.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.057][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.057][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:50.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:50.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.058][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:50.059][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:50.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.059][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.059][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:50.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:50.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.060][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:50.061][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:50.061][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.061][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.061][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:50.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:50.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.063][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:50.073][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-02-10 18:16:50.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:50.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:50.076][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:50.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:50.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:50.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:50.078][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:50.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:50.079][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-02-10 18:16:50.079][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:50.080][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-02-10 18:16:50.081][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:50.081][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml".
biodb.DEBUG[2025-02-10 18:16:50.082][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:50.082][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:50.083][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:50.083][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:50.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:50.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:50.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:50.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:50.086][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:50.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:50.087][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.087][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.088][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.089][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:50.090][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:50.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.090][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.090][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:50.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:50.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.095][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:50.096][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:50.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.097][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.098][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:50.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:50.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.099][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:50.099][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:50.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.100][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.100][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:50.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:50.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.101][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:50.102][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:50.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.102][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:50.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:50.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.104][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:50.104][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:50.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.105][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.105][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:50.106][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.106][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.107][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:50.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.108][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.108][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.109][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.110][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:50.110][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:50.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.111][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.111][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:50.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:50.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.112][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:50.112][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:50.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.113][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.113][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:50.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:50.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.114][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:50.115][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:50.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.115][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.115][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:50.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:50.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.120][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:50.127][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-02-10 18:16:50.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:50.132][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:50.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:50.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:50.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:50.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:50.138][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:50.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:50.138][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-02-10 18:16:50.139][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:50.139][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-02-10 18:16:50.139][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:16:50.140][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml".
biodb.DEBUG[2025-02-10 18:16:50.140][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:50.141][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:50.141][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:50.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:50.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:50.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:50.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:50.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:50.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:50.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:50.146][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.146][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.147][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.148][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:50.148][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:50.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.149][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.149][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:50.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:50.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.150][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:50.151][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:50.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.151][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.151][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:50.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:50.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.152][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:50.153][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:50.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.153][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.153][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:50.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:50.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.155][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:50.155][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:50.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.155][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.156][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:50.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:50.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.157][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:50.157][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:50.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.157][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.158][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:50.158][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.159][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.159][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:50.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.160][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.160][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.161][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.162][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:50.162][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:50.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.163][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.163][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:50.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:50.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.164][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:50.164][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:50.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.165][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.165][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:50.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:50.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.166][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:50.167][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:50.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.167][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.167][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:50.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:50.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:50.181][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-02-10 18:16:50.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:50.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:50.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:50.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:50.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:50.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:50.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:50.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:50.188][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-02-10 18:16:50.188][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:50.189][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.INFO [2025-02-10 18:16:50.189][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-02-10 18:16:50.189][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 18:16:50.190][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 18:16:50.190][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:50.190][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:16:50.191][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 18:16:50.191][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 18:16:50.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:50.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:50.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:50.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:50.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:50.195][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:50.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:50.195][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-02-10 18:16:50.196][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:16:50.197][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:16:50.197][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-02-10 18:16:50.592][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-02-10 18:16:50.945][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-02-10 18:16:50.946][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-02-10 18:16:50.946][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-02-10 18:16:50.950][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-02-10 18:16:50.951][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-02-10 18:16:50.952][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 18:16:50.953][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:50.953][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:50.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:50.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:50.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:50.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:50.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:50.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:50.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:50.958][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.959][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.959][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.964][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:50.965][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:50.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.965][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.965][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:50.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:50.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.967][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:50.967][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:50.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.967][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.968][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:50.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:50.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.969][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:50.969][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:50.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.969][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.970][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:50.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:50.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.971][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:50.971][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:50.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.972][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:50.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:50.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.973][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:50.973][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:50.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.974][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.974][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:50.974][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.975][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.975][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:50.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.976][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.976][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.977][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:50.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.978][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:50.978][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:50.979][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.979][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.979][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:50.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:50.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.980][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:50.980][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:50.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.981][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.981][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:50.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:50.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.982][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:50.983][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:50.983][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.983][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.983][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:50.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:50.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:50.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:50.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:50.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:50.994][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-02-10 18:16:50.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.998][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:50.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:50.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:50.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:51.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:51.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:51.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:51.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:51.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:51.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:51.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:51.002][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-02-10 18:16:51.003][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:51.003][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-02-10 18:16:51.003][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 18:16:51.004][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 18:16:51.004][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:51.004][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:16:51.005][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 18:16:51.005][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 18:16:51.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:51.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:51.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:51.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:51.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:51.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:51.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:51.012][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-02-10 18:16:51.017][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:16:51.017][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:16:51.022][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-02-10 18:16:51.381][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-02-10 18:16:51.749][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:16:51.750][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-02-10 18:16:51.751][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-02-10 18:16:51.752][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-02-10 18:16:51.753][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 18:16:51.753][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:51.753][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:51.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:51.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:51.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:51.757][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:51.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:51.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:51.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:51.758][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:51.762][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:51.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.763][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:51.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:51.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.765][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:51.765][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:51.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.766][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.766][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:51.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:51.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.767][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:51.767][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:51.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.768][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.768][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:51.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:51.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.769][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:51.770][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:51.770][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.770][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.771][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:51.771][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:51.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.771][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.772][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:51.772][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:51.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.772][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.773][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:51.773][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:51.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.774][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.774][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:51.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:51.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.775][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:51.775][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:51.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.776][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:51.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:51.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.777][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:51.777][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:51.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.778][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.778][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:51.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:51.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.779][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:51.780][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:51.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.780][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.780][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:51.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:51.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.781][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:51.782][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:51.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.782][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:51.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:51.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:51.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:51.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:51.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:51.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:51.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:51.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:51.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:51.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:51.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:51.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:51.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:51.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:51.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:51.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:51.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:51.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:51.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:51.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:51.793][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-02-10 18:16:51.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:51.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:51.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:51.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:51.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:51.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:51.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:51.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:51.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:51.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:51.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:51.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:51.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:51.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:51.802][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:51.802][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[2025-02-10 18:16:51.802][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-02-10 18:16:51.803][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:51.803][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-02-10 18:16:51.803][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 18:16:51.804][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 18:16:51.804][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:51.804][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:16:51.805][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 18:16:51.805][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 18:16:51.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:51.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:51.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:51.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:51.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:51.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:51.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:51.809][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-02-10 18:16:51.810][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:16:51.810][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:16:51.810][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-02-10 18:16:52.180][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-02-10 18:16:52.522][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:16:52.522][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-02-10 18:16:52.524][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-02-10 18:16:52.525][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-02-10 18:16:52.525][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 18:16:52.525][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:52.526][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:52.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:52.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:52.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:52.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:52.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:52.529][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:52.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:52.530][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:52.530][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:52.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.531][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:52.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:52.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.532][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:52.533][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:52.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.533][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.534][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:52.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:52.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.535][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:52.535][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:52.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.535][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.536][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:52.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:52.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.537][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:52.537][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:52.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.538][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.538][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:52.538][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:52.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.539][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.539][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:52.539][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:52.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.540][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.540][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:52.540][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:52.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.541][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.541][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:52.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:52.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.542][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:52.543][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:52.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.543][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:52.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:52.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.545][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:52.545][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:52.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.546][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.546][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:52.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:52.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.551][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:52.552][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:52.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.552][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.552][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:52.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:52.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.553][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:52.554][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:52.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.554][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:52.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:52.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:52.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:52.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:52.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:52.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:52.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:52.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:52.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:52.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:52.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:52.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:52.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:52.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:52.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:52.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:52.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:52.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:52.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:52.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:52.565][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-02-10 18:16:52.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:52.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:52.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:52.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:52.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:52.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:52.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:52.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:52.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:52.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:52.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:52.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:52.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:52.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:52.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:52.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:52.572][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-02-10 18:16:52.573][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:52.573][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-02-10 18:16:52.573][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 18:16:52.574][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 18:16:52.574][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:52.575][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:16:52.575][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 18:16:52.575][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 18:16:52.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:52.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:52.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:52.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:52.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:52.579][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:52.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:52.580][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-02-10 18:16:52.580][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:16:52.581][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:16:52.581][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-02-10 18:16:52.960][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-02-10 18:16:53.311][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:16:53.312][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-02-10 18:16:53.314][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-02-10 18:16:53.314][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-02-10 18:16:53.315][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 18:16:53.315][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:53.316][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:53.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:53.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:53.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:53.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:53.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:53.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:53.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:53.324][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:53.324][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:53.324][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.325][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:53.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:53.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.326][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:53.326][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:53.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.327][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.327][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:53.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:53.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.328][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:53.329][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:53.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.329][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.330][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:53.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:53.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.331][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:53.331][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:53.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.331][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.332][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:53.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:53.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.333][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:53.333][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:53.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.334][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.334][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:53.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:53.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.335][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:53.335][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:53.335][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.336][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.336][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:53.336][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:53.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.337][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.337][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:53.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:53.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.338][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:53.338][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:53.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.339][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:53.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:53.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.340][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:53.341][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:53.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.341][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.341][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:53.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:53.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.343][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:53.343][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:53.343][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.343][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.344][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:53.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:53.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.345][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:53.345][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:53.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.346][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.346][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:53.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:53.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:53.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:53.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:53.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:53.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:53.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:53.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:53.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:53.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:53.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:53.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:53.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:53.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:53.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:53.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:53.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:53.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:53.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:53.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:53.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:53.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:53.362][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-02-10 18:16:53.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:53.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:53.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:53.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:53.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:53.365][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:53.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:53.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:53.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:53.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:53.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:53.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:53.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:53.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:53.369][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:53.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:53.369][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-02-10 18:16:53.370][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:53.370][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-02-10 18:16:53.371][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 18:16:53.371][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 18:16:53.371][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:53.371][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:16:53.372][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 18:16:53.372][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 18:16:53.373][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:53.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:53.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:53.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:53.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:53.376][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:53.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:53.376][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-02-10 18:16:53.377][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:16:53.377][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:16:53.378][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-02-10 18:16:53.760][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-02-10 18:16:54.114][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:16:54.114][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-02-10 18:16:54.116][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-02-10 18:16:54.117][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-02-10 18:16:54.117][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 18:16:54.118][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:54.118][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:54.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:54.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:54.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:54.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:54.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:54.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:54.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:54.123][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:54.123][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:54.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.124][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:54.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:54.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.125][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:54.126][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:54.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.126][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.126][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:54.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:54.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.127][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:54.128][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:54.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.128][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.129][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:54.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:54.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.130][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:54.130][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:54.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.130][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:54.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:54.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.132][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:54.132][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:54.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.132][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.133][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:54.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:54.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.137][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:54.138][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:54.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.138][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.138][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:54.139][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:54.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.139][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.140][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:54.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:54.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.141][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:54.141][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:54.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.141][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:54.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:54.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.143][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:54.143][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:54.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.143][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.144][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:54.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:54.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.145][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:54.145][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:54.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.146][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.146][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:54.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:54.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.147][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:54.147][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:54.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.148][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.148][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:54.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:54.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:54.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:54.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:54.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:54.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:54.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:54.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:54.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:54.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:54.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:54.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:54.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:54.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:54.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:54.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:54.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:54.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:54.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:54.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:54.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:54.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:54.159][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-02-10 18:16:54.159][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:54.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:54.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:54.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:54.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.161][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:54.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:54.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:54.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:54.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:54.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:54.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:54.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:54.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:54.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:54.166][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-02-10 18:16:54.167][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:54.167][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-02-10 18:16:54.167][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 18:16:54.168][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 18:16:54.168][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:54.168][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:16:54.169][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 18:16:54.169][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 18:16:54.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:54.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:54.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:54.175][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:54.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:54.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:54.175][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[2025-02-10 18:16:54.176][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-02-10 18:16:54.176][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:16:54.177][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:16:54.177][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-02-10 18:16:54.569][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-02-10 18:16:54.934][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:16:54.935][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-02-10 18:16:54.936][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-02-10 18:16:54.937][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-02-10 18:16:54.938][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 18:16:54.938][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:54.938][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:54.939][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:54.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:54.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:54.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:54.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:54.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:54.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:54.943][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:54.943][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:54.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.944][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:54.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:54.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.945][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:54.945][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:54.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.946][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.946][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:54.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:54.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.947][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:54.948][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:54.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.948][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.948][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:54.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:54.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.950][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:54.950][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:54.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.950][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.951][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:54.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:54.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.952][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:54.952][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:54.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.952][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:54.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:54.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.954][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:54.954][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:54.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.955][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.955][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:54.955][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:54.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.956][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.956][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:54.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:54.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.957][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:54.957][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:54.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.958][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:54.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:54.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.959][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:54.959][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:54.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.960][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.960][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:54.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:54.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.961][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:54.962][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:54.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.962][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.962][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:54.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:54.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.963][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:54.964][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:54.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.964][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.969][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:54.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:54.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:54.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:54.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:54.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:54.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:54.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:54.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:54.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:54.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:54.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:54.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:54.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:54.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:54.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:54.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:54.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:54.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:54.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:54.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:54.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:54.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:54.981][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-02-10 18:16:54.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:54.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:54.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:54.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:54.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:54.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:54.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:54.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:54.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:54.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:54.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:54.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:54.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:54.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:54.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:54.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:54.987][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-02-10 18:16:54.988][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:54.988][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-02-10 18:16:54.988][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 18:16:54.989][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 18:16:54.989][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:54.989][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:16:54.990][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 18:16:54.990][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 18:16:54.991][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:54.991][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:54.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:54.993][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:54.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:54.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:54.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:54.994][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-02-10 18:16:54.995][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:16:54.995][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:16:54.995][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-02-10 18:16:55.371][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-02-10 18:16:55.739][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:16:55.740][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-02-10 18:16:55.741][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-02-10 18:16:55.742][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-02-10 18:16:55.743][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 18:16:55.743][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:55.743][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:55.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:55.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:55.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:55.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:55.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:55.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:55.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:55.748][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:55.748][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:55.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.751][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:55.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:55.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.753][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:55.753][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:55.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.754][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.754][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:55.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:55.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.755][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:55.755][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:55.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.756][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:55.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:55.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.757][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:55.757][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:55.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.758][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.758][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:55.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:55.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.759][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:55.759][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:55.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.759][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.760][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:55.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:55.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.761][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:55.761][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:55.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.761][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.762][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:55.762][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:55.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.762][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.763][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:55.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:55.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.763][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:55.764][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:55.764][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.764][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:55.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:55.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.765][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:55.765][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:55.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.766][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:55.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:55.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.767][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:55.767][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:55.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.768][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.768][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:55.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:55.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.769][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:55.769][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:55.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.769][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.770][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:55.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:55.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:55.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:55.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:55.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:55.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:55.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:55.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:55.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:55.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:55.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:55.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:55.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:55.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:55.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:55.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:55.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:55.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:55.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:55.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:55.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:55.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:55.781][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-02-10 18:16:55.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:55.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:55.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:55.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:55.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:55.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:55.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:55.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:55.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:55.784][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:55.785][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:55.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:55.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:55.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:55.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:55.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:55.787][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-02-10 18:16:55.788][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:55.788][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-02-10 18:16:55.788][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 18:16:55.789][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 18:16:55.789][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:55.789][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:16:55.789][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 18:16:55.790][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 18:16:55.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:55.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:55.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:55.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:55.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:55.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:55.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:55.793][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-02-10 18:16:55.794][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:16:55.794][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:16:55.794][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-02-10 18:16:56.186][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-02-10 18:16:56.540][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:16:56.541][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-02-10 18:16:56.542][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-02-10 18:16:56.543][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-02-10 18:16:56.544][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 18:16:56.544][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:56.544][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:56.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:56.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:56.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:56.547][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:56.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:56.547][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:56.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:56.548][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:56.548][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:56.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.549][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:56.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:56.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.550][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:56.550][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:56.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.551][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.551][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:56.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:56.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.552][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:56.552][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:56.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.553][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.553][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:56.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:56.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.554][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:56.554][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:56.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.555][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.555][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:56.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:56.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.556][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:56.556][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:56.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.557][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.557][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:56.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:56.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.558][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:56.558][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:56.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.559][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.559][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:56.559][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:56.562][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.563][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.563][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:56.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:56.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.564][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:56.564][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:56.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.565][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.565][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:56.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:56.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.566][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:56.566][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:56.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.567][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.567][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:56.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:56.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.568][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:56.568][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:56.569][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.569][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.569][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:56.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:56.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.570][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:56.570][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:56.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.571][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.571][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:56.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:56.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:56.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:56.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:56.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:56.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:56.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:56.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:56.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:56.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:56.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:56.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:56.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:56.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:56.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:56.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:56.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:56.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:56.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:56.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:56.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:56.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:56.581][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-02-10 18:16:56.581][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:56.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:56.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.582][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:56.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:56.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:56.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:56.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:56.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:56.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:56.584][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:56.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:56.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:56.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:56.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:56.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:56.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:56.587][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-02-10 18:16:56.587][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:56.588][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-02-10 18:16:56.588][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 18:16:56.588][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 18:16:56.589][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:56.589][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:16:56.589][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 18:16:56.589][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 18:16:56.590][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:56.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:56.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:56.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:56.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:56.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:56.595][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[2025-02-10 18:16:56.595][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-02-10 18:16:56.596][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:16:56.596][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:16:56.597][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-02-10 18:16:57.006][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-02-10 18:16:57.353][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:16:57.354][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-02-10 18:16:57.355][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-02-10 18:16:57.356][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-02-10 18:16:57.357][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 18:16:57.357][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:57.358][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:57.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:57.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:57.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:57.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:57.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:57.361][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:57.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:57.362][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:57.362][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:57.362][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.363][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:57.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:57.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.364][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:57.364][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:57.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.365][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.365][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:57.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:57.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.366][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:57.367][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:57.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.367][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.368][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:57.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:57.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.369][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:57.369][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:57.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.369][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.370][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:57.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:57.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.371][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:57.371][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:57.371][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.371][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:57.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:57.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.373][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:57.373][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:57.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.374][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.374][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:57.374][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:57.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.375][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.375][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:57.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:57.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.376][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:57.376][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:57.377][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.377][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:57.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:57.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.378][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:57.378][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:57.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.379][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.379][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:57.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:57.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.380][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:57.381][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:57.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.381][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.381][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:57.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:57.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.382][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:57.383][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:57.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.383][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.384][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:57.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:57.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.385][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:57.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:57.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:57.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:57.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:57.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:57.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:57.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:57.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:57.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:57.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:57.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:57.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:57.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:57.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:57.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:57.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:57.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:57.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:57.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:57.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:57.399][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-02-10 18:16:57.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:57.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:57.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:57.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:57.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:57.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:57.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:57.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:57.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:57.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:57.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:57.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:57.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:57.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:57.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:57.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:57.405][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-02-10 18:16:57.406][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:16:57.406][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-02-10 18:16:57.407][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 18:16:57.407][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 18:16:57.407][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:16:57.407][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:16:57.408][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 18:16:57.408][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 18:16:57.409][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:57.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:57.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:57.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:57.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:57.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:57.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:16:57.412][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-02-10 18:16:57.413][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:16:57.413][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:16:57.413][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-02-10 18:16:57.810][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-02-10 18:16:58.158][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:16:58.159][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-02-10 18:16:58.160][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-02-10 18:16:58.161][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-02-10 18:16:58.161][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 18:16:58.162][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:16:58.162][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:16:58.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:16:58.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:16:58.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:16:58.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:16:58.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:16:58.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:16:58.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:16:58.166][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:58.167][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:58.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.167][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:58.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:58.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.169][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:58.172][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:58.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.174][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.174][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:16:58.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:16:58.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.176][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:58.176][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:58.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.176][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.177][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:16:58.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:16:58.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.178][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:58.178][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:58.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.178][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.179][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:16:58.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:16:58.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.180][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:58.180][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:58.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.181][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.181][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:16:58.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:16:58.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.182][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:58.182][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:16:58.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.183][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.183][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:58.183][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:58.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.184][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.184][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:16:58.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:58.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.185][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:58.185][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:58.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.186][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:58.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:16:58.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.187][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:58.187][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:58.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.187][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.188][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:16:58.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:16:58.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.189][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:58.189][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:58.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.189][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.190][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:16:58.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:16:58.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.191][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:58.191][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:58.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.191][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.191][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:16:58.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:16:58.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:58.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:58.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:58.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:58.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:58.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:58.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:16:58.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:16:58.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:58.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:58.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:58.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:58.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:58.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:58.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:58.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:58.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:58.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:58.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:16:58.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:16:58.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:58.201][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-02-10 18:16:58.202][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:58.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:58.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.202][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:58.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:58.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:16:58.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:58.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:16:58.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:16:58.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:16:58.213][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:16:58.214][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:16:58.214][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:16:58.214][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-10 18:17:01.990][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-10 18:17:05.251][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:05.252][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-02-10 18:17:05.253][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-02-10 18:17:05.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.264][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.267][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.269][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.270][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.272][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.274][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.298][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.305][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.311][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.313][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.314][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.324][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.326][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.342][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.349][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.350][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.350][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.359][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.365][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.370][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.371][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.374][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.375][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.380][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:05.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:05.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:05.388][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:05.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:05.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:05.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:05.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.393][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:05.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:05.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:05.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:05.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:05.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:05.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:05.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.403][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:05.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:05.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:05.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:05.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:05.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:05.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:05.413][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:05.414][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:05.414][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:05.415][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-10 18:17:05.778][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-10 18:17:06.161][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:06.162][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-02-10 18:17:06.163][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-02-10 18:17:06.165][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:06.166][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:06.166][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:06.167][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-10 18:17:06.518][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-10 18:17:06.886][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:06.887][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-02-10 18:17:06.888][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-02-10 18:17:06.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:06.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:06.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:06.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:06.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:06.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:06.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:06.893][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-02-10 18:17:06.896][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:17:06.898][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-02-10 18:17:06.899][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 18:17:06.899][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 18:17:06.899][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:17:06.900][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:17:06.900][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 18:17:06.900][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 18:17:06.901][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:06.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:06.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:06.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:06.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:06.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:06.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:06.905][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-02-10 18:17:06.906][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:06.906][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:06.906][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-02-10 18:17:07.316][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-02-10 18:17:07.684][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:07.685][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-02-10 18:17:07.686][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-02-10 18:17:07.687][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-02-10 18:17:07.688][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 18:17:07.688][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:17:07.688][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:17:07.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:07.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:07.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:07.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:07.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:07.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:07.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:07.693][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:07.693][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:07.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.693][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:07.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:07.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.695][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:17:07.695][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:17:07.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.696][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.696][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:17:07.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:17:07.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.697][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:17:07.697][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:17:07.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.698][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.699][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:17:07.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:17:07.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.700][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:17:07.700][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:17:07.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.701][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.701][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:17:07.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:17:07.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.702][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:17:07.703][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:17:07.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.703][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.703][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:17:07.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:17:07.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.704][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:07.705][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:07.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.705][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.705][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:07.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:07.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.706][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:17:07.707][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:07.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.707][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.708][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:17:07.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:07.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.709][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:07.709][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:07.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.709][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:07.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:07.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.711][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:17:07.711][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:17:07.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.711][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.712][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:17:07.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:17:07.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.717][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:17:07.717][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:17:07.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.718][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.718][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:17:07.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:17:07.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.719][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:17:07.720][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:17:07.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.720][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.720][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:17:07.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:17:07.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.721][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:07.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:07.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:07.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:07.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:07.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:07.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:07.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:07.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:07.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:07.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:07.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:07.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:07.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:07.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:07.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:07.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:07.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:07.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:07.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:07.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:07.731][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-02-10 18:17:07.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:07.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:07.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:07.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:07.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:07.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:07.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:07.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:07.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:07.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:07.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:07.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:07.737][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:07.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:07.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:07.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:07.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:07.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:07.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:07.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:07.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:07.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:07.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:07.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:07.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:07.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:07.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:07.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:07.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:07.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:07.744][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-02-10 18:17:07.744][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:17:07.745][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-02-10 18:17:07.745][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 18:17:07.745][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 18:17:07.746][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:17:07.746][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:17:07.746][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 18:17:07.746][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 18:17:07.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:07.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:07.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:07.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:07.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:07.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:07.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:07.753][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-02-10 18:17:07.754][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:07.754][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:07.755][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-02-10 18:17:08.153][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-02-10 18:17:08.508][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:08.509][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-02-10 18:17:08.510][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-02-10 18:17:08.511][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-02-10 18:17:08.511][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 18:17:08.512][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:17:08.512][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:17:08.513][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.515][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.517][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:08.517][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:08.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.518][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:08.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:08.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.519][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:17:08.519][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:17:08.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.520][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.520][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:17:08.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:17:08.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.521][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:17:08.521][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:17:08.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.522][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.522][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:17:08.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:17:08.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.523][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:17:08.523][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:17:08.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.524][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.524][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:17:08.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:17:08.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.525][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:17:08.526][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:17:08.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.526][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.526][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:17:08.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:17:08.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.527][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:08.528][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:08.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.528][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.528][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:17:08.529][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:08.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.529][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.529][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:17:08.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:08.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.531][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.531][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.531][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.533][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:17:08.533][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:17:08.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.533][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.534][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:17:08.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:17:08.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.535][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:17:08.535][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:17:08.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.536][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.536][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:17:08.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:17:08.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.537][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:17:08.537][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:17:08.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.538][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.538][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:17:08.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:17:08.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:08.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:08.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.544][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:08.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:08.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:08.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:08.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:08.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:08.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:08.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:08.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:08.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:08.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:08.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:08.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:08.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:08.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:08.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:08.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:08.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:08.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.554][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-02-10 18:17:08.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.555][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.564][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:08.565][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:17:08.565][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-10 18:17:08.565][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:17:08.566][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-02-10 18:17:08.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.573][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.573][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.576][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.591][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.593][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.605][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.607][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.611][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.628][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.631][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.631][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.634][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.639][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.643][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.645][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.652][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.660][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.674][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.684][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.688][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.694][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.694][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.711][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:08.712][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:17:08.713][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-10 18:17:08.713][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:17:08.713][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-02-10 18:17:08.714][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.717][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.732][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.748][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.752][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.769][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.770][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.776][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.782][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.793][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.794][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.818][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.820][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.824][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.835][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.848][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:08.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:08.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.858][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-02-10 18:17:08.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-02-10 18:17:08.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-10 18:17:08.861][biodb::testThat]
biodb.INFO [2025-02-10 18:17:08.861][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-02-10 18:17:08.861][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:17:08.861][biodb::testThat]
biodb.TRACE[2025-02-10 18:17:08.862][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-10 18:17:08.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-10 18:17:08.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:08.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:08.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.864][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:08.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:08.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:08.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:08.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:08.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:08.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:08.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:08.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:08.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:08.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:08.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:08.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:08.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:08.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:08.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:08.872][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:08.873][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:08.873][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:08.876][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-10 18:17:09.227][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-10 18:17:09.575][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:09.576][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-02-10 18:17:09.577][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-02-10 18:17:09.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:09.579][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:09.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:09.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:09.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:09.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:09.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:09.582][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:09.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:09.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:09.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:09.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:09.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:09.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:09.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:09.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:09.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:09.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:09.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:09.585][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:09.586][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:09.586][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:09.587][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-10 18:17:09.949][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-10 18:17:12.825][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:12.826][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-02-10 18:17:12.827][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-02-10 18:17:12.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:12.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:12.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:12.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:12.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:12.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:12.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:12.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:12.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:12.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:12.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:12.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:12.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:12.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:12.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:12.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:12.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:12.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:12.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:12.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:12.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:12.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:12.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:12.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:12.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:12.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:12.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:12.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:12.842][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-10 18:17:12.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:12.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:12.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:12.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:12.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:12.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:12.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:12.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.848][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:12.848][private$selectFields]
biodb.TRACE[2025-02-10 18:17:12.848][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 18:17:12.849][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 18:17:12.849][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:12.853][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.854][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.855][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.855][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.855][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.856][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.856][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:12.856][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:12.856][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.857][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.857][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.858][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 18:17:12.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.864][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-02-10 18:17:12.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:12.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:12.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:12.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:12.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:12.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:12.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:12.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.870][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:12.870][private$selectFields]
biodb.TRACE[2025-02-10 18:17:12.870][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 18:17:12.870][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 18:17:12.871][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:12.871][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.871][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.872][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.872][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.872][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.873][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.873][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:12.873][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:12.873][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.874][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.874][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.874][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.874][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 18:17:12.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.886][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-10 18:17:12.887][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:12.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:12.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:12.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:12.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:12.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:12.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:12.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.896][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:12.896][private$selectFields]
biodb.TRACE[2025-02-10 18:17:12.897][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 18:17:12.897][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 18:17:12.897][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:12.897][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.898][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.898][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.898][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.898][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.899][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.899][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.901][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.902][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:12.902][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:12.902][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.903][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.903][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.903][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 18:17:12.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.905][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.906][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:12.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.907][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-02-10 18:17:12.907][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-10 18:17:12.907][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-10 18:17:12.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:12.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:12.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:12.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:12.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:12.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:12.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:12.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:12.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:12.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:12.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:12.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:12.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:12.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:13.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:13.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:13.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:13.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:13.014][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:13.015][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:13.015][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:13.016][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-10 18:17:13.365][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-10 18:17:13.709][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:13.710][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-02-10 18:17:13.711][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-02-10 18:17:13.713][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:13.714][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:13.714][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:13.715][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-10 18:17:14.087][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-10 18:17:14.437][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:14.438][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-02-10 18:17:14.440][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-02-10 18:17:14.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.447][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.450][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.457][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.459][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.469][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-10 18:17:14.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.484][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.484][private$selectFields]
biodb.TRACE[2025-02-10 18:17:14.484][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 18:17:14.485][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 18:17:14.485][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.485][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.485][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.486][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.486][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.487][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.487][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.487][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.488][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.488][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.488][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.489][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.489][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 18:17:14.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.493][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-02-10 18:17:14.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.497][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.TRACE[2025-02-10 18:17:14.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.503][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.512][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.512][private$selectFields]
biodb.TRACE[2025-02-10 18:17:14.512][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 18:17:14.513][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 18:17:14.513][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.513][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.514][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.517][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.517][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.518][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.518][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.519][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.523][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.524][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.524][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.524][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.525][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 18:17:14.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.529][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-10 18:17:14.529][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.540][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.540][private$selectFields]
biodb.TRACE[2025-02-10 18:17:14.541][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 18:17:14.541][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 18:17:14.541][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.541][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.542][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.542][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.542][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.543][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.543][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.543][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.544][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.544][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.544][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.545][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.545][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 18:17:14.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.548][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-02-10 18:17:14.548][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-10 18:17:14.549][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-10 18:17:14.552][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-02-10 18:17:14.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-02-10 18:17:14.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-10 18:17:14.554][biodb::testThat]
biodb.INFO [2025-02-10 18:17:14.554][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-02-10 18:17:14.555][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:17:14.555][biodb::testThat]
biodb.TRACE[2025-02-10 18:17:14.556][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-10 18:17:14.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-10 18:17:14.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.560][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.562][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.564][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:14.566][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:14.567][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:17:14.567][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-02-10 18:17:14.567][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:17:14.568][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-02-10 18:17:14.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.575][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:14.576][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:17:14.577][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-02-10 18:17:14.577][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:17:14.578][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-02-10 18:17:14.579][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.579][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.582][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.589][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.592][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-10 18:17:14.593][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.598][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.599][private$selectFields]
biodb.TRACE[2025-02-10 18:17:14.599][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 18:17:14.599][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 18:17:14.600][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.600][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.600][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.601][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.601][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.601][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.602][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.602][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.602][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.603][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.603][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.603][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.604][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 18:17:14.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.607][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-02-10 18:17:14.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.611][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.614][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.614][private$selectFields]
biodb.TRACE[2025-02-10 18:17:14.615][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 18:17:14.615][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 18:17:14.615][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.615][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.616][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.616][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.617][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.617][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.617][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.618][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.618][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.618][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.618][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.619][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.619][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 18:17:14.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.623][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-10 18:17:14.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.626][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.626][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.629][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.630][private$selectFields]
biodb.TRACE[2025-02-10 18:17:14.630][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 18:17:14.630][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 18:17:14.630][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.631][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.631][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.631][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.631][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.632][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.632][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.632][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.633][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.633][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.633][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.633][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.634][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.634][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.634][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 18:17:14.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.642][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-02-10 18:17:14.642][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-10 18:17:14.642][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-10 18:17:14.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.651][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.653][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:14.654][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:14.655][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:17:14.656][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-02-10 18:17:14.656][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:17:14.656][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-02-10 18:17:14.657][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:14.658][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:17:14.659][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-02-10 18:17:14.659][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:17:14.659][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-02-10 18:17:14.660][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.666][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.673][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.679][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-10 18:17:14.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.699][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.699][private$selectFields]
biodb.TRACE[2025-02-10 18:17:14.699][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 18:17:14.700][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 18:17:14.700][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.700][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.701][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.701][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.701][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.702][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.702][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.702][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.703][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.703][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.703][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.704][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.704][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 18:17:14.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.705][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.708][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-02-10 18:17:14.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.708][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.714][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.714][private$selectFields]
biodb.TRACE[2025-02-10 18:17:14.714][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 18:17:14.715][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 18:17:14.715][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.715][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.715][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.716][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.716][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.716][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.717][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.717][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.717][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.718][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.718][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.718][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.719][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 18:17:14.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.721][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.722][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-10 18:17:14.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.725][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.727][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.728][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.728][private$selectFields]
biodb.TRACE[2025-02-10 18:17:14.728][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 18:17:14.729][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 18:17:14.729][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.729][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.729][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.730][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.730][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.730][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.731][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.731][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.731][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.732][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.732][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.732][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.733][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 18:17:14.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.734][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.736][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-02-10 18:17:14.737][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-10 18:17:14.737][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-10 18:17:14.740][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-02-10 18:17:14.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-02-10 18:17:14.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-10 18:17:14.743][biodb::testThat]
biodb.INFO [2025-02-10 18:17:14.743][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-02-10 18:17:14.743][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:17:14.744][biodb::testThat]
biodb.TRACE[2025-02-10 18:17:14.745][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-10 18:17:14.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-10 18:17:14.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.748][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.749][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:14.758][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:14.759][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:17:14.759][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-02-10 18:17:14.760][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:17:14.760][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-02-10 18:17:14.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.764][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.764][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.768][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:14.769][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:17:14.769][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-02-10 18:17:14.769][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:17:14.770][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-02-10 18:17:14.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.773][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.778][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:14.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.786][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-10 18:17:14.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.788][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.791][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.791][private$selectFields]
biodb.TRACE[2025-02-10 18:17:14.792][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 18:17:14.792][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 18:17:14.792][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.793][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.793][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.793][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.794][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.794][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.794][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.795][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.795][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.795][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.795][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.796][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.796][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.796][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 18:17:14.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.800][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-02-10 18:17:14.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.805][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.806][private$selectFields]
biodb.TRACE[2025-02-10 18:17:14.806][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 18:17:14.806][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 18:17:14.807][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.807][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.807][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.808][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.808][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.808][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.809][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.809][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.809][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.809][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.810][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.810][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.810][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 18:17:14.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.814][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-10 18:17:14.814][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.819][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.820][private$selectFields]
biodb.TRACE[2025-02-10 18:17:14.820][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 18:17:14.820][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 18:17:14.820][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.821][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.821][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.821][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.821][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.822][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.822][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.822][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.823][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.823][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.824][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.824][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.824][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.825][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 18:17:14.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.828][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-02-10 18:17:14.828][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-10 18:17:14.829][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-10 18:17:14.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:14.845][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:14.846][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:17:14.846][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-02-10 18:17:14.847][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:17:14.847][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-02-10 18:17:14.848][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:14.849][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:17:14.849][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-02-10 18:17:14.850][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:17:14.850][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-02-10 18:17:14.851][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.854][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.862][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.862][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.865][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.866][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:14.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:14.872][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-10 18:17:14.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.876][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.878][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.878][private$selectFields]
biodb.TRACE[2025-02-10 18:17:14.878][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 18:17:14.878][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 18:17:14.879][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.879][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.879][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.879][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.880][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.880][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.880][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.881][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.881][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.881][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.881][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.882][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.882][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.882][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.882][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 18:17:14.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.886][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-02-10 18:17:14.886][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.892][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.892][private$selectFields]
biodb.TRACE[2025-02-10 18:17:14.892][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 18:17:14.892][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 18:17:14.893][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.893][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.893][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.894][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.894][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.894][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.895][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.895][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.895][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.895][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.896][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.896][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.896][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 18:17:14.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.900][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-10 18:17:14.900][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.903][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:14.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.905][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.906][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.906][private$selectFields]
biodb.TRACE[2025-02-10 18:17:14.906][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-10 18:17:14.907][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-10 18:17:14.907][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.907][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.907][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.908][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.908][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.908][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.909][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.909][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.909][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-10 18:17:14.910][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.910][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.910][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.911][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-10 18:17:14.911][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:14.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:14.914][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-02-10 18:17:14.914][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-10 18:17:14.915][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-10 18:17:14.922][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-02-10 18:17:14.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-02-10 18:17:14.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:14.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-10 18:17:14.925][biodb::testThat]
biodb.INFO [2025-02-10 18:17:14.925][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-02-10 18:17:14.925][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:17:14.926][biodb::testThat]
biodb.DEBUG[2025-02-10 18:17:14.926][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-02-10 18:17:14.926][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:17:14.927][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-02-10 18:17:14.927][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 18:17:14.928][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 18:17:14.928][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:17:14.928][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:17:14.928][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 18:17:14.929][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 18:17:14.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:14.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:14.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:14.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:14.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:14.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:14.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:14.933][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-02-10 18:17:14.934][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:14.934][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:14.934][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-02-10 18:17:15.301][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-02-10 18:17:15.661][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:15.662][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-02-10 18:17:15.663][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-02-10 18:17:15.664][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-02-10 18:17:15.664][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 18:17:15.665][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:17:15.665][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:17:15.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:15.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:15.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:15.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:15.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:15.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:15.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:15.670][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:15.670][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:15.671][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.671][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:15.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:15.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.672][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:17:15.673][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:17:15.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.673][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.674][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:17:15.674][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:17:15.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.674][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.675][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:17:15.675][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:17:15.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.676][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.676][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:17:15.676][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:17:15.676][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.677][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.677][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:15.677][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:15.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.678][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.678][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:17:15.678][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:15.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.679][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.679][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:15.680][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:15.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.680][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.680][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:17:15.681][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:17:15.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.681][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.682][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:17:15.682][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:17:15.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.683][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.683][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:17:15.683][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:17:15.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.684][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:15.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:15.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:15.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:15.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:15.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:15.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:15.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:15.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:15.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:15.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:15.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:15.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:15.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:15.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:15.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:15.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:15.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:15.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:15.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:15.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:15.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:15.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:15.699][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-02-10 18:17:15.699][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-02-10 18:17:15.703][biodb::testThat]
biodb.INFO [2025-02-10 18:17:15.703][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-02-10 18:17:15.704][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:17:15.704][biodb::testThat]
biodb.DEBUG[2025-02-10 18:17:15.708][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-02-10 18:17:15.708][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-02-10 18:17:15.708][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-02-10 18:17:15.709][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-02-10 18:17:15.709][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-02-10 18:17:15.710][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 18:17:15.710][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:17:15.710][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:17:15.710][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 18:17:15.711][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 18:17:15.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:15.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:15.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:15.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:15.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:15.715][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:15.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:15.715][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-02-10 18:17:15.716][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:15.716][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:15.717][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-02-10 18:17:16.071][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-02-10 18:17:16.425][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:16.425][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-02-10 18:17:16.427][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-02-10 18:17:16.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:16.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:16.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:16.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:16.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:16.430][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:16.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:16.431][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-02-10 18:17:16.432][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:16.432][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:16.433][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-02-10 18:17:17.971][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-02-10 18:17:18.330][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:18.331][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-02-10 18:17:18.332][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-02-10 18:17:18.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:18.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:18.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:18.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:18.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:18.336][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:18.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:18.336][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-02-10 18:17:18.337][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:18.338][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:18.338][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-02-10 18:17:18.686][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-02-10 18:17:19.040][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:19.041][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-02-10 18:17:19.042][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-02-10 18:17:19.043][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-02-10 18:17:19.043][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 18:17:19.044][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-02-10 18:17:19.044][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-02-10 18:17:19.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:19.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:19.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:19.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:19.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:19.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:19.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:19.049][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.049][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.050][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.051][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:17:19.051][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:17:19.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.052][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.052][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:17:19.052][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:17:19.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.053][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.053][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:17:19.054][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:17:19.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.054][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.054][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:17:19.055][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:17:19.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.056][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.056][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:19.056][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:19.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.057][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.057][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:17:19.057][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:19.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.058][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.058][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:19.059][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:19.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.059][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.059][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:17:19.060][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:17:19.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.060][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.061][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:17:19.061][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:17:19.061][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.061][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.062][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:17:19.062][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:17:19.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.062][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.063][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:19.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:19.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:19.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:19.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:19.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:19.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:19.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:19.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:19.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:19.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:19.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:19.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:19.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:19.074][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.075][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.075][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.077][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:17:19.077][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:17:19.077][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.077][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.078][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:17:19.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:17:19.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.079][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:17:19.079][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:17:19.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.080][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.080][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:17:19.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:17:19.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.081][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:17:19.081][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:17:19.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.082][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.082][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:17:19.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:17:19.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.083][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:17:19.083][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:17:19.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.084][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.084][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:17:19.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:17:19.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.085][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:19.086][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:19.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.086][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.086][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:19.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:19.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.087][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:17:19.088][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:19.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.088][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.088][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:17:19.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:19.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.089][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:19.090][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:19.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.090][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:19.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:19.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.091][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:17:19.092][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:17:19.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.092][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.092][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:17:19.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:17:19.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.094][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:17:19.094][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:17:19.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.094][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.095][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:17:19.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:17:19.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.096][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:17:19.096][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:17:19.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.096][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.101][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:17:19.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:17:19.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:19.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:19.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:19.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:19.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:19.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:19.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:19.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:19.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:19.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:19.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:19.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:19.112][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:19.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-10 18:17:19.113][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.113][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.114][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.115][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:17:19.116][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:17:19.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.116][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.116][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:17:19.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:17:19.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.117][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:17:19.118][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:17:19.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.118][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.118][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:17:19.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:17:19.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.119][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:17:19.120][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:17:19.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.120][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.120][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:17:19.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:17:19.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.121][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:17:19.122][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:17:19.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.122][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:17:19.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:17:19.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.123][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:19.124][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:19.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.124][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.124][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:19.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:19.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.125][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:17:19.126][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:19.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.126][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.126][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:17:19.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:19.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.127][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:19.128][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:19.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.128][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:19.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:19.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.129][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:17:19.130][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:17:19.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.130][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.130][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:17:19.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:17:19.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.132][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:17:19.132][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:17:19.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.133][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.133][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:17:19.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:17:19.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.134][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:17:19.134][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:17:19.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.135][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.135][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:17:19.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:17:19.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:19.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:19.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:19.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:19.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:19.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:19.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:19.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:19.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:19.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:19.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:19.152][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-02-10 18:17:19.153][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-02-10 18:17:19.153][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-02-10 18:17:19.157][biodb::testThat]
biodb.INFO [2025-02-10 18:17:19.158][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-02-10 18:17:19.158][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:17:19.158][biodb::testThat]
biodb.INFO [2025-02-10 18:17:19.165][biodb::testThat]
biodb.INFO [2025-02-10 18:17:19.166][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-02-10 18:17:19.166][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:17:19.166][biodb::testThat]
biodb.INFO [2025-02-10 18:17:19.169][biodb::testThat]
biodb.INFO [2025-02-10 18:17:19.169][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-02-10 18:17:19.169][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:17:19.169][biodb::testThat]
biodb.DEBUG[2025-02-10 18:17:19.170][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:19.171][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:19.172][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:19.172][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-02-10 18:17:19.665][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-02-10 18:17:21.450][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:21.451][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-02-10 18:17:21.452][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-02-10 18:17:21.456][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:17:21.457][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:17:21.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:21.457][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:21.458][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:21.458][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:21.458][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:21.458][ef$get] fields variable is a list.
biodb.INFO [2025-02-10 18:17:21.459][biodb::testThat]
biodb.INFO [2025-02-10 18:17:21.459][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-02-10 18:17:21.459][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:17:21.460][biodb::testThat]
biodb.ERROR[2025-02-10 18:17:21.465][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-02-10 18:17:21.470][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-02-10 18:17:21.478][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-10 18:17:21.478][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-02-10 18:17:21.479][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-02-10 18:17:21.479][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-10 18:17:21.479][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:21.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:21.480][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.480][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-10 18:17:21.484][biodb::testContext]
biodb.INFO [2025-02-10 18:17:21.484][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-10 18:17:21.484][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-02-10 18:17:21.484][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-10 18:17:21.485][biodb::testContext]
biodb.INFO [2025-02-10 18:17:21.485][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-10 18:17:21.486][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-10 18:17:21.487][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 18:17:21.488][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-10 18:17:21.488][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-10 18:17:21.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.489][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-10 18:17:21.489][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-10 18:17:21.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.490][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[2025-02-10 18:17:21.490][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-10 18:17:21.490][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-10 18:17:21.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.491][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-10 18:17:21.492][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-10 18:17:21.492][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-10 18:17:21.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.493][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-10 18:17:21.493][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-10 18:17:21.493][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-10 18:17:21.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.494][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-10 18:17:21.494][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-10 18:17:21.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.495][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[2025-02-10 18:17:21.495][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-10 18:17:21.496][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-10 18:17:21.496][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-10 18:17:21.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.497][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-10 18:17:21.497][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-10 18:17:21.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.498][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-10 18:17:21.498][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-10 18:17:21.498][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-10 18:17:21.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.499][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-10 18:17:21.500][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-10 18:17:21.500][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-10 18:17:21.500][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-10 18:17:21.500][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-10 18:17:21.501][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-10 18:17:21.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.502][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-10 18:17:21.502][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-10 18:17:21.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.503][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-10 18:17:21.503][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-10 18:17:21.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.504][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-10 18:17:21.504][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-10 18:17:21.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.505][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-10 18:17:21.505][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-10 18:17:21.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.506][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[2025-02-10 18:17:21.506][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-10 18:17:21.506][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-10 18:17:21.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.507][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-10 18:17:21.507][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-10 18:17:21.512][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-10 18:17:21.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.513][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[2025-02-10 18:17:21.513][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-10 18:17:21.514][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-10 18:17:21.514][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-10 18:17:21.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.515][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-10 18:17:21.515][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:21.516][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-10 18:17:21.516][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.516][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:17:21.516][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.517][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:17:21.517][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:21.517][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 18:17:21.518][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-10 18:17:21.518][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:17:21.518][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.518][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-10 18:17:21.519][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:17:21.519][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:21.519][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.519][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 18:17:21.519][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 18:17:21.519][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 18:17:21.519][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-10 18:17:21.519][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-10 18:17:21.520][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 18:17:21.520][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:21.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:21.520][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:17:21.521][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:21.521][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:21.521][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:17:21.521][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:21.522][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:17:21.522][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:17:21.522][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:21.522][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:21.523][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-10 18:17:21.523][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:21.523][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-10 18:17:21.524][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.524][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:17:21.524][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.524][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:17:21.525][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:21.525][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 18:17:21.525][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-10 18:17:21.525][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:17:21.526][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.526][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-10 18:17:21.526][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:17:21.526][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:21.527][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.527][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 18:17:21.527][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 18:17:21.527][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 18:17:21.527][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-10 18:17:21.527][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-10 18:17:21.527][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 18:17:21.527][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:21.528][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:21.528][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:17:21.528][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:21.528][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:21.529][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:17:21.529][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:21.529][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:17:21.530][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:17:21.530][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:21.530][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:21.530][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-10 18:17:21.531][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.531][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-10 18:17:21.531][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.532][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:17:21.532][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.532][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:17:21.532][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:21.533][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 18:17:21.533][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-10 18:17:21.533][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:17:21.533][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:21.534][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-10 18:17:21.534][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:17:21.534][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:21.534][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.535][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:21.535][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 18:17:21.535][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:21.535][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:21.536][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:17:21.536][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:21.536][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:21.536][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:17:21.537][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:21.537][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:17:21.537][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:17:21.537][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:21.537][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:21.538][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-10 18:17:21.538][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.538][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-10 18:17:21.539][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.539][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:17:21.539][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.539][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:17:21.540][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:21.540][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 18:17:21.540][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-10 18:17:21.540][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:17:21.541][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:21.541][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-10 18:17:21.541][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:17:21.541][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:21.542][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.542][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:21.542][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 18:17:21.542][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:21.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:21.543][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:17:21.543][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:21.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:21.544][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:17:21.544][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:21.544][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:17:21.544][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:17:21.545][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:21.545][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:21.545][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 18:17:21.545][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.547][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[2025-02-10 18:17:21.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.554][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[2025-02-10 18:17:21.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.558][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[2025-02-10 18:17:21.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.565][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-10 18:17:21.565][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-10 18:17:21.565][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-10 18:17:21.566][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-10 18:17:21.568][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-10 18:17:21.569][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-10 18:17:21.569][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-10 18:17:21.570][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-10 18:17:21.570][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-10 18:17:21.570][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-10 18:17:21.571][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-10 18:17:21.571][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-10 18:17:21.571][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-10 18:17:21.572][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-10 18:17:21.572][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-10 18:17:21.572][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-10 18:17:21.573][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-10 18:17:21.573][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-10 18:17:21.573][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-10 18:17:21.574][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-10 18:17:21.574][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-10 18:17:21.574][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-10 18:17:21.575][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-10 18:17:21.575][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-10 18:17:21.576][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-10 18:17:21.576][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-10 18:17:21.576][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-10 18:17:21.577][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-10 18:17:21.577][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-10 18:17:21.577][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-10 18:17:21.578][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-10 18:17:21.578][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-10 18:17:21.578][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-10 18:17:21.579][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-10 18:17:21.579][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-10 18:17:21.579][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-10 18:17:21.580][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-10 18:17:21.580][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-10 18:17:21.580][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-10 18:17:21.581][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-10 18:17:21.581][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-10 18:17:21.581][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-10 18:17:21.582][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-10 18:17:21.582][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-10 18:17:21.583][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-10 18:17:21.583][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-10 18:17:21.583][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-10 18:17:21.584][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-10 18:17:21.584][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-10 18:17:21.584][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-10 18:17:21.585][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-10 18:17:21.585][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-10 18:17:21.585][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-10 18:17:21.586][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-10 18:17:21.586][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-10 18:17:21.586][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-10 18:17:21.587][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-10 18:17:21.587][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-10 18:17:21.587][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-10 18:17:21.588][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-10 18:17:21.588][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-10 18:17:21.588][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-10 18:17:21.589][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-10 18:17:21.589][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-10 18:17:21.589][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-10 18:17:21.590][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-10 18:17:21.590][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-10 18:17:21.590][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-10 18:17:21.591][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-10 18:17:21.591][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-10 18:17:21.592][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-10 18:17:21.592][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-10 18:17:21.592][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-10 18:17:21.593][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-10 18:17:21.593][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-10 18:17:21.593][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-10 18:17:21.594][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-10 18:17:21.594][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-10 18:17:21.594][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-10 18:17:21.595][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-10 18:17:21.595][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-10 18:17:21.595][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-10 18:17:21.596][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-10 18:17:21.596][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-10 18:17:21.597][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-10 18:17:21.597][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 18:17:21.597][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.598][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.598][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[2025-02-10 18:17:21.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:21.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:21.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:21.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:21.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:21.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:21.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:21.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:21.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.607][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[2025-02-10 18:17:21.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:21.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:21.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:21.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:21.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.610][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[2025-02-10 18:17:21.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:21.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:21.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.612][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[2025-02-10 18:17:21.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:21.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:21.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:21.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:21.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:21.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:21.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.618][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[2025-02-10 18:17:21.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:21.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:21.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.619][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.DEBUG[2025-02-10 18:17:21.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:21.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:21.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:21.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:21.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.622][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[2025-02-10 18:17:21.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:21.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:21.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:21.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:21.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:21.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:21.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:21.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:21.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:21.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:21.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:21.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:21.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:21.629][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-02-10 18:17:21.630][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-02-10 18:17:21.630][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:21.631][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-10 18:17:21.631][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.631][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:17:21.631][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.632][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:17:21.632][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.632][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-02-10 18:17:21.633][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-10 18:17:21.633][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:17:21.633][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.633][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-02-10 18:17:21.634][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:17:21.634][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-02-10 18:17:21.634][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-02-10 18:17:21.634][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-02-10 18:17:21.634][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-02-10 18:17:21.634][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-02-10 18:17:21.634][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-02-10 18:17:21.634][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-02-10 18:17:21.634][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-02-10 18:17:21.634][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-02-10 18:17:21.634][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-02-10 18:17:21.634][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-02-10 18:17:21.634][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:21.634][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 18:17:21.634][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 18:17:21.634][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 18:17:21.635][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-10 18:17:21.635][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:21.635][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:21.635][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:17:21.636][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:21.636][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:21.636][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:17:21.636][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:17:21.636][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-02-10 18:17:21.637][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:17:21.637][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:17:21.637][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:21.637][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-02-10 18:17:21.637][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-02-10 18:17:21.638][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-10 18:17:21.638][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-10 18:17:21.639][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-02-10 18:17:21.639][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-10 18:17:21.640][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-10 18:17:21.640][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-10 18:17:21.641][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-02-10 18:17:21.641][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-02-10 18:17:21.642][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-02-10 18:17:21.642][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-02-10 18:17:21.642][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-10 18:17:21.643][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-10 18:17:21.643][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-02-10 18:17:21.643][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-02-10 18:17:21.644][biodb::testThat]
biodb.INFO [2025-02-10 18:17:21.644][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-02-10 18:17:21.644][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:17:21.644][biodb::testThat]
biodb.DEBUG[2025-02-10 18:17:21.646][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-02-10 18:17:21.647][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:21.647][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:21.648][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-02-10 18:17:21.985][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-02-10 18:17:22.480][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:22.481][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-02-10 18:17:22.482][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-02-10 18:17:22.484][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:22.485][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:22.485][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:22.486][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-02-10 18:17:22.834][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-02-10 18:17:23.176][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:23.177][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-02-10 18:17:23.178][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-02-10 18:17:23.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:23.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:23.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:23.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:23.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:23.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:23.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:23.186][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:23.187][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:23.187][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:23.188][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-02-10 18:17:23.530][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-02-10 18:17:23.881][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:23.882][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-02-10 18:17:23.883][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-02-10 18:17:23.884][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:23.884][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:23.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:23.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:23.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:23.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:23.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:23.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:23.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:23.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:23.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:23.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:23.895][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:23.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:23.896][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:23.897][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:17:23.898][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-02-10 18:17:23.898][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:17:23.898][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-02-10 18:17:23.899][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:23.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:23.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:23.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:23.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:23.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:23.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:23.902][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:23.903][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:17:23.903][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-02-10 18:17:23.904][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:17:23.904][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-02-10 18:17:23.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:23.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:23.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:23.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:23.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:23.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:23.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:23.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:23.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:23.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:23.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:23.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:23.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:23.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:23.911][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:23.912][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:17:23.913][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-02-10 18:17:23.913][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:17:23.914][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-02-10 18:17:23.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:23.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:23.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:23.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:23.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:23.917][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:23.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:23.918][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:23.919][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:17:23.919][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-02-10 18:17:23.920][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:17:23.920][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-02-10 18:17:23.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:23.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:23.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:23.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:23.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:23.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:23.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:23.924][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:23.925][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:23.925][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:23.926][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-02-10 18:17:24.270][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-02-10 18:17:24.617][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:24.618][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-02-10 18:17:24.619][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-02-10 18:17:24.620][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:24.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:24.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:24.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:24.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:24.622][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:24.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-10 18:17:24.625][biodb::testThat]
biodb.INFO [2025-02-10 18:17:24.625][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-02-10 18:17:24.625][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:17:24.625][biodb::testThat]
biodb.DEBUG[2025-02-10 18:17:24.626][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:24.627][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:24.627][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:24.628][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-02-10 18:17:26.918][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-02-10 18:17:27.284][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:27.285][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-02-10 18:17:27.286][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-02-10 18:17:27.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:27.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:27.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:27.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:27.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:27.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:27.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:27.291][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:27.292][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:27.292][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:27.293][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-02-10 18:17:27.638][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-02-10 18:17:28.003][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:28.004][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-02-10 18:17:28.005][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-02-10 18:17:28.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:28.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.009][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.009][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.INFO [2025-02-10 18:17:28.011][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-10 18:17:28.011][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-02-10 18:17:28.011][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-02-10 18:17:28.012][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-10 18:17:28.012][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.012][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.013][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-10 18:17:28.014][biodb::testContext]
biodb.INFO [2025-02-10 18:17:28.014][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-10 18:17:28.015][biodb::testContext] Test context - Test web services
biodb.INFO [2025-02-10 18:17:28.015][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-10 18:17:28.015][biodb::testContext]
biodb.INFO [2025-02-10 18:17:28.016][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-10 18:17:28.016][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-10 18:17:28.018][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 18:17:28.018][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-10 18:17:28.018][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-10 18:17:28.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.019][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-10 18:17:28.020][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-10 18:17:28.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.021][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-10 18:17:28.021][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-10 18:17:28.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.022][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-10 18:17:28.022][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-10 18:17:28.022][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-10 18:17:28.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.023][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[2025-02-10 18:17:28.023][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-10 18:17:28.024][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-10 18:17:28.024][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-10 18:17:28.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.025][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-10 18:17:28.025][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-10 18:17:28.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.026][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-10 18:17:28.026][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-10 18:17:28.027][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-10 18:17:28.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.028][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-10 18:17:28.028][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-10 18:17:28.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.029][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-10 18:17:28.029][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-10 18:17:28.029][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-10 18:17:28.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.030][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-10 18:17:28.030][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-10 18:17:28.031][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-10 18:17:28.031][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-10 18:17:28.031][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-10 18:17:28.031][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-10 18:17:28.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.032][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[2025-02-10 18:17:28.032][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-10 18:17:28.033][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-10 18:17:28.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.036][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-10 18:17:28.040][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-10 18:17:28.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.041][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-10 18:17:28.041][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-10 18:17:28.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.042][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-10 18:17:28.042][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-10 18:17:28.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.043][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.DEBUG[2025-02-10 18:17:28.043][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-10 18:17:28.043][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-10 18:17:28.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.044][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-10 18:17:28.045][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-10 18:17:28.050][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-10 18:17:28.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.051][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[2025-02-10 18:17:28.051][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-10 18:17:28.052][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-10 18:17:28.052][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-10 18:17:28.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.053][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-10 18:17:28.053][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.054][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-10 18:17:28.054][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.054][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:17:28.054][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.055][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.055][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.055][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.055][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-10 18:17:28.055][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:17:28.056][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.056][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-10 18:17:28.056][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:17:28.056][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.057][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.057][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 18:17:28.057][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 18:17:28.057][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 18:17:28.057][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-10 18:17:28.057][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-10 18:17:28.057][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 18:17:28.057][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:28.058][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:28.058][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:17:28.058][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:28.058][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:28.058][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.059][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.059][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:17:28.059][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:17:28.059][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.060][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.060][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-10 18:17:28.060][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.061][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-10 18:17:28.061][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.061][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:17:28.061][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.061][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.062][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.062][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.062][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-10 18:17:28.062][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:17:28.063][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.063][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-10 18:17:28.063][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:17:28.063][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.064][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.064][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 18:17:28.064][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 18:17:28.064][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 18:17:28.064][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-10 18:17:28.064][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-10 18:17:28.064][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 18:17:28.064][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:28.064][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:28.065][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:17:28.065][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:28.065][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:28.065][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.066][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.066][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:17:28.066][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:17:28.066][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.066][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.067][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-10 18:17:28.067][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.067][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-10 18:17:28.068][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.068][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:17:28.068][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.068][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.069][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.069][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.069][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-10 18:17:28.069][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:17:28.070][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.070][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-10 18:17:28.070][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:17:28.070][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.070][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.071][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.071][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 18:17:28.071][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:28.071][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:28.072][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:17:28.072][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:28.072][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:28.072][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.072][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.073][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:17:28.073][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:17:28.073][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.073][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.074][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-10 18:17:28.074][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.074][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-10 18:17:28.074][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.075][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:17:28.075][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.075][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.075][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.076][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.076][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-10 18:17:28.076][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:17:28.076][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.077][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-10 18:17:28.077][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:17:28.077][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.077][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.078][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.078][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 18:17:28.078][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:28.078][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:28.078][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:17:28.079][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:28.079][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:28.079][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.079][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.080][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:17:28.080][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:17:28.080][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.080][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.081][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 18:17:28.081][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.085][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[2025-02-10 18:17:28.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.099][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-10 18:17:28.099][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-10 18:17:28.099][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-10 18:17:28.100][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-10 18:17:28.100][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-10 18:17:28.100][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-10 18:17:28.101][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-10 18:17:28.101][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-10 18:17:28.101][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-10 18:17:28.102][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-10 18:17:28.102][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-10 18:17:28.102][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-10 18:17:28.103][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-10 18:17:28.103][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-10 18:17:28.103][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-10 18:17:28.104][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-10 18:17:28.104][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-10 18:17:28.105][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-10 18:17:28.105][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-10 18:17:28.105][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-10 18:17:28.106][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-10 18:17:28.106][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-10 18:17:28.106][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-10 18:17:28.107][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-10 18:17:28.107][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-10 18:17:28.107][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-10 18:17:28.108][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-10 18:17:28.108][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-10 18:17:28.108][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-10 18:17:28.109][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-10 18:17:28.109][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-10 18:17:28.109][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-10 18:17:28.110][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-10 18:17:28.110][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-10 18:17:28.110][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-10 18:17:28.111][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-10 18:17:28.111][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-10 18:17:28.111][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-10 18:17:28.112][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-10 18:17:28.112][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-10 18:17:28.112][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-10 18:17:28.113][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-10 18:17:28.113][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-10 18:17:28.113][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-10 18:17:28.114][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-10 18:17:28.114][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-10 18:17:28.114][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-10 18:17:28.115][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-10 18:17:28.115][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-10 18:17:28.115][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-10 18:17:28.116][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-10 18:17:28.116][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-10 18:17:28.116][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-10 18:17:28.117][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-10 18:17:28.117][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-10 18:17:28.117][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-10 18:17:28.118][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-10 18:17:28.118][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-10 18:17:28.119][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-10 18:17:28.119][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-10 18:17:28.119][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-10 18:17:28.120][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-10 18:17:28.120][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-10 18:17:28.120][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-10 18:17:28.121][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-10 18:17:28.121][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-10 18:17:28.124][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-10 18:17:28.124][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-10 18:17:28.124][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-10 18:17:28.124][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-10 18:17:28.125][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-10 18:17:28.125][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-10 18:17:28.125][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-10 18:17:28.126][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-10 18:17:28.126][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-10 18:17:28.126][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-10 18:17:28.127][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-10 18:17:28.127][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-10 18:17:28.127][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-10 18:17:28.128][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-10 18:17:28.128][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-10 18:17:28.128][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-10 18:17:28.129][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-10 18:17:28.129][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-10 18:17:28.130][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-10 18:17:28.130][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 18:17:28.130][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.131][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.132][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.DEBUG[2025-02-10 18:17:28.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.140][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[2025-02-10 18:17:28.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.150][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[2025-02-10 18:17:28.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.155][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-02-10 18:17:28.155][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-02-10 18:17:28.156][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.156][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.156][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.157][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:17:28.157][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.157][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.157][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.158][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-02-10 18:17:28.158][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-10 18:17:28.158][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:17:28.158][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.159][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-02-10 18:17:28.159][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:17:28.159][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-02-10 18:17:28.159][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-02-10 18:17:28.159][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-02-10 18:17:28.159][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-02-10 18:17:28.159][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-02-10 18:17:28.159][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-02-10 18:17:28.159][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-02-10 18:17:28.159][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-02-10 18:17:28.159][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-02-10 18:17:28.159][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-02-10 18:17:28.159][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-02-10 18:17:28.159][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.160][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 18:17:28.160][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 18:17:28.160][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 18:17:28.160][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-10 18:17:28.160][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:28.160][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:28.160][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:17:28.161][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:28.161][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:28.161][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.161][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:17:28.161][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-02-10 18:17:28.162][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:17:28.162][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:17:28.162][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.162][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-02-10 18:17:28.162][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-02-10 18:17:28.163][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-10 18:17:28.163][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-10 18:17:28.163][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-02-10 18:17:28.164][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-10 18:17:28.164][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-10 18:17:28.164][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-10 18:17:28.165][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-02-10 18:17:28.166][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-02-10 18:17:28.166][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-02-10 18:17:28.166][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-02-10 18:17:28.167][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-10 18:17:28.167][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-10 18:17:28.167][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-02-10 18:17:28.167][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-02-10 18:17:28.168][biodb::testThat]
biodb.INFO [2025-02-10 18:17:28.168][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-02-10 18:17:28.168][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:17:28.168][biodb::testThat]
biodb.DEBUG[2025-02-10 18:17:28.169][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-02-10 18:17:28.170][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:17:28.171][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-02-10 18:17:28.171][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:17:28.172][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-02-10 18:17:28.173][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:28.174][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:28.174][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:28.174][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-02-10 18:17:28.516][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-02-10 18:17:28.862][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:28.862][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-02-10 18:17:28.864][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-02-10 18:17:28.867][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-10 18:17:28.867][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-02-10 18:17:28.867][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-02-10 18:17:28.868][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-10 18:17:28.868][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.868][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.869][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-10 18:17:28.870][biodb::testContext]
biodb.INFO [2025-02-10 18:17:28.870][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-10 18:17:28.871][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-02-10 18:17:28.871][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-10 18:17:28.871][biodb::testContext]
biodb.INFO [2025-02-10 18:17:28.872][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-10 18:17:28.872][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-10 18:17:28.874][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 18:17:28.874][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-10 18:17:28.874][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-10 18:17:28.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.875][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-10 18:17:28.876][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-10 18:17:28.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.877][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-10 18:17:28.877][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-10 18:17:28.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.878][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-10 18:17:28.878][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-10 18:17:28.878][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-10 18:17:28.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.879][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-10 18:17:28.880][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-10 18:17:28.880][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-10 18:17:28.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.881][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-10 18:17:28.881][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-10 18:17:28.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.882][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-10 18:17:28.882][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-10 18:17:28.882][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-10 18:17:28.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.883][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-10 18:17:28.884][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-10 18:17:28.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.884][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-10 18:17:28.885][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-10 18:17:28.885][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-10 18:17:28.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.886][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.DEBUG[2025-02-10 18:17:28.886][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-10 18:17:28.886][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-10 18:17:28.886][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-10 18:17:28.887][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-10 18:17:28.887][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-10 18:17:28.887][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-10 18:17:28.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.888][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-10 18:17:28.888][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-10 18:17:28.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.889][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[2025-02-10 18:17:28.889][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-10 18:17:28.890][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-10 18:17:28.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.890][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-10 18:17:28.891][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-10 18:17:28.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.892][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-10 18:17:28.892][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-10 18:17:28.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.897][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-10 18:17:28.897][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-10 18:17:28.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.898][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-10 18:17:28.898][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-10 18:17:28.904][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-10 18:17:28.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.905][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-10 18:17:28.906][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-10 18:17:28.906][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-10 18:17:28.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.907][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-10 18:17:28.907][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.908][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-10 18:17:28.908][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.908][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:17:28.908][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.909][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.909][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.909][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.909][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-10 18:17:28.910][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:17:28.910][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.910][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-10 18:17:28.910][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:17:28.911][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.911][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.911][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 18:17:28.911][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 18:17:28.911][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 18:17:28.911][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-10 18:17:28.911][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-10 18:17:28.911][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 18:17:28.912][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:28.912][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:28.912][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:17:28.912][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:28.912][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:28.913][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.913][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.913][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:17:28.913][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:17:28.914][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.914][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.914][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-10 18:17:28.915][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.915][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-10 18:17:28.915][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.915][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:17:28.916][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.916][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.916][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.916][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.917][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-10 18:17:28.917][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:17:28.917][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.917][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-10 18:17:28.918][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:17:28.918][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.918][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.918][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 18:17:28.918][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 18:17:28.918][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 18:17:28.918][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-10 18:17:28.918][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-10 18:17:28.919][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 18:17:28.919][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:28.919][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:28.919][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:17:28.920][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:28.920][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:28.920][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.920][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.920][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:17:28.921][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:17:28.921][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.921][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.921][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-10 18:17:28.922][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.922][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-10 18:17:28.922][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.923][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:17:28.923][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.923][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.923][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.924][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.924][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-10 18:17:28.924][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:17:28.924][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.925][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-10 18:17:28.925][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:17:28.925][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.925][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.926][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.926][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 18:17:28.926][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:28.926][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:28.927][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:17:28.927][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:28.927][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:28.927][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.927][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.928][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:17:28.928][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:17:28.928][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.928][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.929][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-10 18:17:28.929][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.929][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-10 18:17:28.930][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.930][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:17:28.930][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.930][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.931][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.931][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.931][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-10 18:17:28.931][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:17:28.932][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.932][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-10 18:17:28.932][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:17:28.932][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.933][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:28.933][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.933][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-10 18:17:28.933][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:28.934][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:28.934][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:17:28.934][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:28.934][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:28.935][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:17:28.935][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.935][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:17:28.935][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:17:28.936][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:28.936][self$setPropertyValue]
biodb.DEBUG[2025-02-10 18:17:28.936][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 18:17:28.936][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.938][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[2025-02-10 18:17:28.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.940][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[2025-02-10 18:17:28.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.941][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[2025-02-10 18:17:28.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.954][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[2025-02-10 18:17:28.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.955][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[2025-02-10 18:17:28.955][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-10 18:17:28.956][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-10 18:17:28.956][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-10 18:17:28.957][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-10 18:17:28.957][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-10 18:17:28.957][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-10 18:17:28.958][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-10 18:17:28.958][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-10 18:17:28.958][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-10 18:17:28.959][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-10 18:17:28.959][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-10 18:17:28.959][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-10 18:17:28.960][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-10 18:17:28.960][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-10 18:17:28.961][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-10 18:17:28.961][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-10 18:17:28.961][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-10 18:17:28.962][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-10 18:17:28.962][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-10 18:17:28.962][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-10 18:17:28.963][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-10 18:17:28.963][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-10 18:17:28.963][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-10 18:17:28.964][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-10 18:17:28.964][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-10 18:17:28.964][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-10 18:17:28.965][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-10 18:17:28.965][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-10 18:17:28.966][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-10 18:17:28.966][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-10 18:17:28.966][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-10 18:17:28.967][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-10 18:17:28.967][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-10 18:17:28.967][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-10 18:17:28.968][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-10 18:17:28.968][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-10 18:17:28.968][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-10 18:17:28.969][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-10 18:17:28.969][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-10 18:17:28.970][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-10 18:17:28.970][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-10 18:17:28.970][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-10 18:17:28.971][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-10 18:17:28.971][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-10 18:17:28.971][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-10 18:17:28.972][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-10 18:17:28.972][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-10 18:17:28.972][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-10 18:17:28.973][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-10 18:17:28.973][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-10 18:17:28.974][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-10 18:17:28.974][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-10 18:17:28.974][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-10 18:17:28.975][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-10 18:17:28.975][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-10 18:17:28.975][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-10 18:17:28.976][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-10 18:17:28.976][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-10 18:17:28.976][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-10 18:17:28.977][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-10 18:17:28.977][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-10 18:17:28.977][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-10 18:17:28.978][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-10 18:17:28.978][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-10 18:17:28.979][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-10 18:17:28.979][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-10 18:17:28.979][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-10 18:17:28.980][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-10 18:17:28.980][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-10 18:17:28.980][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-10 18:17:28.981][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-10 18:17:28.981][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-10 18:17:28.984][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-10 18:17:28.984][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-10 18:17:28.985][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-10 18:17:28.985][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-10 18:17:28.985][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-10 18:17:28.986][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-10 18:17:28.986][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-10 18:17:28.986][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-10 18:17:28.987][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-10 18:17:28.987][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-10 18:17:28.987][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-10 18:17:28.988][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-10 18:17:28.988][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-10 18:17:28.989][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-10 18:17:28.989][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.989][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.997][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.DEBUG[2025-02-10 18:17:28.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:28.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:28.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:28.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:28.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:28.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:28.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:28.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:29.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:29.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:29.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:29.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:29.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:29.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:29.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:29.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:29.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:29.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:29.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:29.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:29.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:29.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:29.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:29.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:29.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:29.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:29.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:29.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:29.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:29.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:29.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:29.005][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[2025-02-10 18:17:29.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:29.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:29.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:29.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:29.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:29.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:29.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:29.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:29.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:29.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:29.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:29.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:29.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:29.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:29.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:29.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:29.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:29.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:29.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:29.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:29.009][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[2025-02-10 18:17:29.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:29.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:29.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:29.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:29.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:29.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:29.011][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[2025-02-10 18:17:29.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:29.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:29.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:29.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:29.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:29.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:29.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:29.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:29.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:29.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:29.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:29.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:29.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:29.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:29.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-10 18:17:29.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:29.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:29.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:29.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:29.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:29.015][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[2025-02-10 18:17:29.016][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-02-10 18:17:29.016][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-02-10 18:17:29.017][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:29.017][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-10 18:17:29.017][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:29.018][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-10 18:17:29.018][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:29.018][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-10 18:17:29.018][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:29.019][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-02-10 18:17:29.019][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-10 18:17:29.019][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-10 18:17:29.019][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:29.020][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-02-10 18:17:29.020][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-10 18:17:29.020][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-02-10 18:17:29.020][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-02-10 18:17:29.020][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-02-10 18:17:29.020][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-02-10 18:17:29.020][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-02-10 18:17:29.020][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-02-10 18:17:29.020][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-02-10 18:17:29.020][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-02-10 18:17:29.020][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-02-10 18:17:29.020][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-02-10 18:17:29.020][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-02-10 18:17:29.021][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-10 18:17:29.021][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-10 18:17:29.021][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-10 18:17:29.021][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-10 18:17:29.021][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-10 18:17:29.021][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:29.022][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:29.022][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-10 18:17:29.022][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-10 18:17:29.022][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-10 18:17:29.023][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-10 18:17:29.023][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:17:29.023][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-02-10 18:17:29.023][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-10 18:17:29.023][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-10 18:17:29.023][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-10 18:17:29.024][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-02-10 18:17:29.024][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-02-10 18:17:29.024][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-10 18:17:29.025][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-10 18:17:29.025][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-02-10 18:17:29.025][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-10 18:17:29.026][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-10 18:17:29.026][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-10 18:17:29.027][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-02-10 18:17:29.027][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-02-10 18:17:29.028][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-02-10 18:17:29.028][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-02-10 18:17:29.029][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-10 18:17:29.029][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-10 18:17:29.029][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-02-10 18:17:29.029][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-02-10 18:17:29.030][biodb::testThat]
biodb.INFO [2025-02-10 18:17:29.030][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-02-10 18:17:29.030][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-10 18:17:29.031][biodb::testThat]
biodb.DEBUG[2025-02-10 18:17:29.032][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-02-10 18:17:29.033][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:17:29.033][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-02-10 18:17:29.033][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:17:29.034][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-02-10 18:17:29.035][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-10 18:17:29.036][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-10 18:17:29.037][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-02-10 18:17:29.037][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-10 18:17:29.037][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-02-10 18:17:29.039][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-02-10 18:17:29.039][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-10 18:17:29.039][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-02-10 18:17:29.040][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-10 18:17:29.040][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-10 18:17:29.040][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-10 18:17:29.041][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-10 18:17:29.041][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-10 18:17:29.041][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-10 18:17:29.042][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:29.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:29.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:29.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:29.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:29.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:29.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-10 18:17:29.045][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-02-10 18:17:29.046][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-10 18:17:29.046][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-10 18:17:29.047][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-02-10 18:17:30.826][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-02-10 18:17:31.988][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-10 18:17:31.989][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-02-10 18:17:31.991][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-02-10 18:17:31.991][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-02-10 18:17:31.992][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-10 18:17:31.992][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-10 18:17:31.993][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-10 18:17:31.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-10 18:17:31.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:31.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:31.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:31.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:31.996][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:31.997][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[2025-02-10 18:17:31.998][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:31.998][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:31.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:31.999][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:31.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:32.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:32.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.001][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:17:32.001][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:17:32.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.002][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.002][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-10 18:17:32.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-10 18:17:32.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.003][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:17:32.003][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:17:32.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.004][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.004][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-10 18:17:32.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-10 18:17:32.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.006][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-10 18:17:32.006][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-10 18:17:32.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.006][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.007][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-10 18:17:32.007][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-10 18:17:32.008][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.008][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.008][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:32.008][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:32.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.009][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.009][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:32.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-10 18:17:32.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.011][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:17:32.011][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:32.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.011][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.012][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-10 18:17:32.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-10 18:17:32.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.013][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:32.013][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:32.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.014][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:32.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-10 18:17:32.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.016][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:17:32.016][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:17:32.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.016][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.020][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-10 18:17:32.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-10 18:17:32.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.021][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:17:32.022][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:17:32.022][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.022][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.023][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-10 18:17:32.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-10 18:17:32.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.024][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:17:32.024][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:17:32.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.025][ef$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.025][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-10 18:17:32.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-10 18:17:32.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:32.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:32.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:32.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:32.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:32.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:32.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-10 18:17:32.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-10 18:17:32.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:32.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:32.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:32.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:32.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:32.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:32.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:32.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:32.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:32.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:32.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-10 18:17:32.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-10 18:17:32.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-10 18:17:32.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-10 18:17:32.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-10 18:17:32.037][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-02-10 18:17:32.038][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-10 18:17:32.039][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-02-10 18:17:32.039][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-02-10 18:17:32.039][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-10 18:17:32.039][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-10 18:17:32.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-10 18:17:32.040][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-10 18:17:32.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-10 18:17:32.041][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-10 18:17:32.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 375 ]
> 
> proc.time()
   user  system elapsed 
  5.139   0.359  47.241

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn0.7500.2531.789
ChebiEntry0.1060.0060.113