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This page was generated on 2024-10-18 20:41 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
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 204/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_19
git_last_commit: 323ed25
git_last_commit_date: 2024-04-30 11:39:02 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for biodbLipidmaps on kjohnson1

To the developers/maintainers of the biodbLipidmaps package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbLipidmaps.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: biodbLipidmaps
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
StartedAt: 2024-10-17 14:03:55 -0400 (Thu, 17 Oct 2024)
EndedAt: 2024-10-17 14:06:00 -0400 (Thu, 17 Oct 2024)
EllapsedTime: 124.3 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbLipidmaps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.10.0’
* 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 ‘biodbLipidmaps’ 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 whether startup messages can be suppressed ... 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

biodbLipidmaps.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘biodbLipidmaps’ ...
** 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
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-10-17 14:04:53.629][biodb::testContext]
biodb.INFO [2024-10-17 14:04:53.633][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:04:53.634][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-10-17 14:04:53.635][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:04:53.637][biodb::testContext]
biodb.INFO [2024-10-17 14:04:53.645][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:04:53.647][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 14:04:53.657][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:53.659][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 14:04:53.661][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 14:04:53.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:53.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:53.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:53.665][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 14:04:53.710][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 14:04:53.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:53.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:53.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:53.716][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 14:04:53.717][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 14:04:53.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:53.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:53.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:53.720][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 14:04:53.720][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 14:04:53.721][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 14:04:53.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:53.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:53.723][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.DEBUG[2024-10-17 14:04:53.724][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 14:04:53.724][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 14:04:53.725][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 14:04:53.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:53.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:53.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:53.728][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 14:04:53.728][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 14:04:53.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:53.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:53.730][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[2024-10-17 14:04:53.731][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 14:04:53.732][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 14:04:53.733][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 14:04:53.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:53.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:53.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:53.736][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 14:04:53.736][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 14:04:53.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:53.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:53.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:53.739][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 14:04:53.740][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 14:04:53.742][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 14:04:53.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:53.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:53.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:53.746][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:04:53.747][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 14:04:53.748][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 14:04:53.749][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 14:04:53.749][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 14:04:53.750][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 14:04:53.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:53.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:53.753][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[2024-10-17 14:04:53.753][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 14:04:53.755][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 14:04:53.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:53.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:53.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:53.758][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 14:04:53.759][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 14:04:53.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:53.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:53.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:53.761][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 14:04:53.763][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 14:04:53.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:53.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:53.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:53.783][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 14:04:53.785][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 14:04:53.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:53.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:53.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:53.791][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 14:04:53.791][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 14:04:53.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:53.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:53.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:53.796][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:04:53.797][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 14:04:53.819][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 14:04:53.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:53.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:53.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:53.824][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 14:04:53.825][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 14:04:53.827][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 14:04:53.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:53.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:53.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:53.834][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 14:04:53.874][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:53.897][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-17 14:04:53.898][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:53.899][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:53.899][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:53.900][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:53.900][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:53.901][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:53.901][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:04:53.902][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:53.902][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:53.903][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 14:04:53.904][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:53.906][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:53.907][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:53.908][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:53.908][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:04:53.908][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:04:53.908][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:04:53.908][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:04:53.910][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:53.911][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:53.913][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:53.914][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:53.915][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:53.916][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:53.916][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:53.917][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:53.919][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:53.921][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:53.922][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:53.923][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:53.925][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 14:04:53.927][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:53.928][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:04:53.930][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:53.931][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:53.945][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:53.949][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:53.951][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:53.952][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:53.954][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:04:53.954][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:53.955][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:53.956][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 14:04:53.956][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:53.957][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:53.958][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:53.958][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:53.958][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:04:53.958][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:04:53.958][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:04:53.958][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:04:53.965][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:53.966][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:53.967][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:53.969][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:53.970][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:53.970][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:53.971][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:53.971][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:53.972][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:53.972][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:53.973][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:53.973][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:53.974][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 14:04:53.975][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:53.975][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-17 14:04:53.976][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:53.976][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:53.977][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:53.977][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:53.978][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:53.978][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:53.979][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:04:53.979][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:53.980][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:53.980][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 14:04:53.980][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:53.981][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:53.982][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:53.982][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:53.983][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:53.984][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:53.984][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:53.985][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:53.985][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:53.986][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:53.986][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:53.987][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:53.987][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:53.988][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:53.989][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:53.989][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:53.990][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 14:04:53.991][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:53.992][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:04:53.992][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:53.993][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:53.994][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:53.994][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:53.995][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:53.995][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:53.996][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:04:53.997][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:53.997][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:53.998][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 14:04:53.998][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:53.999][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:53.999][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:54.000][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:54.001][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:54.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:54.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:54.002][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:54.003][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:54.003][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:54.004][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:54.004][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:54.007][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:54.008][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:54.008][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:54.009][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:54.015][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:54.016][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.020][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[2024-10-17 14:04:54.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.043][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[2024-10-17 14:04:54.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.052][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[2024-10-17 14:04:54.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.084][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[2024-10-17 14:04:54.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.088][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[2024-10-17 14:04:54.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.091][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[2024-10-17 14:04:54.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.095][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[2024-10-17 14:04:54.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.103][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 14:04:54.109][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 14:04:54.111][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 14:04:54.113][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 14:04:54.115][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 14:04:54.118][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 14:04:54.119][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 14:04:54.121][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 14:04:54.122][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 14:04:54.123][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 14:04:54.125][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 14:04:54.143][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 14:04:54.147][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 14:04:54.149][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 14:04:54.150][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 14:04:54.152][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 14:04:54.153][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 14:04:54.154][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 14:04:54.155][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 14:04:54.157][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 14:04:54.158][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 14:04:54.159][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 14:04:54.164][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 14:04:54.176][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 14:04:54.179][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 14:04:54.182][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 14:04:54.183][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 14:04:54.184][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 14:04:54.186][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 14:04:54.187][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 14:04:54.189][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 14:04:54.190][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 14:04:54.191][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 14:04:54.192][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 14:04:54.194][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 14:04:54.195][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 14:04:54.196][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 14:04:54.198][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 14:04:54.199][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 14:04:54.200][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 14:04:54.202][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 14:04:54.203][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 14:04:54.204][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 14:04:54.205][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 14:04:54.206][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 14:04:54.207][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 14:04:54.208][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 14:04:54.212][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 14:04:54.214][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 14:04:54.215][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 14:04:54.217][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 14:04:54.218][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 14:04:54.219][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 14:04:54.221][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 14:04:54.240][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 14:04:54.244][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 14:04:54.245][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 14:04:54.246][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 14:04:54.247][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 14:04:54.249][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 14:04:54.250][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 14:04:54.251][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 14:04:54.252][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 14:04:54.254][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 14:04:54.255][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 14:04:54.257][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 14:04:54.259][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 14:04:54.260][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 14:04:54.261][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 14:04:54.262][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 14:04:54.263][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 14:04:54.266][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 14:04:54.267][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 14:04:54.270][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 14:04:54.272][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 14:04:54.274][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 14:04:54.275][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 14:04:54.277][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 14:04:54.278][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 14:04:54.279][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 14:04:54.280][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 14:04:54.281][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 14:04:54.283][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 14:04:54.287][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 14:04:54.289][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:04:54.292][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:54.293][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.294][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:54.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:54.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:54.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:54.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:54.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:54.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:54.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:54.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.320][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.DEBUG[2024-10-17 14:04:54.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:54.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:54.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.344][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.DEBUG[2024-10-17 14:04:54.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:54.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:54.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:54.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:54.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:54.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:54.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:54.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:54.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:54.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:54.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:54.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:54.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:54.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:54.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:54.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:54.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:54.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:54.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:54.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:54.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:54.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:54.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.411][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[2024-10-17 14:04:54.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:54.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:54.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:54.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:54.419][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-10-17 14:04:54.430][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-10-17 14:04:54.444][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:54.445][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 14:04:54.446][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:54.447][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:54.447][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:54.448][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:54.449][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:54.450][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:54.451][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:04:54.452][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:54.453][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:54.454][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-10-17 14:04:54.454][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:54.455][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-10-17 14:04:54.455][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-10-17 14:04:54.455][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-10-17 14:04:54.455][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-10-17 14:04:54.455][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-10-17 14:04:54.455][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-10-17 14:04:54.455][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-10-17 14:04:54.455][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-10-17 14:04:54.455][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-10-17 14:04:54.456][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:54.457][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:54.457][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:04:54.458][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:54.459][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:54.460][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:54.461][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:54.462][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:54.463][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:54.464][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:54.464][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-17 14:04:54.464][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-10-17 14:04:54.465][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:54.466][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:54.467][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:54.468][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:54.474][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-10-17 14:04:54.475][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 14:04:54.507][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-10-17 14:04:54.509][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-10-17 14:04:54.514][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-10-17 14:04:54.520][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-10-17 14:04:54.540][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-17 14:04:54.541][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-17 14:04:54.542][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-10-17 14:04:54.543][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-10-17 14:04:54.552][biodb::testThat]
biodb.INFO [2024-10-17 14:04:54.553][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-10-17 14:04:54.553][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:54.554][biodb::testThat]
biodb.TRACE[2024-10-17 14:04:54.558][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-10-17 14:04:54.559][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:04:54.562][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-17 14:04:54.572][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:54.572][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:54.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:54.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:54.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:54.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:54.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:54.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:54.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:54.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:54.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:54.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:54.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:54.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.639][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:54.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:54.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.642][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:54.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:54.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.660][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:54.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:54.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.689][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:54.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:54.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.710][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:54.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:54.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.714][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:54.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:54.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.716][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 14:04:54.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:54.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.720][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 14:04:54.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:54.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.724][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:54.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:54.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.728][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:54.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:54.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.731][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:54.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:54.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.735][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:54.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:54.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.738][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 14:04:54.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:54.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.742][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-17 14:04:54.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:54.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.745][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:54.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:54.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.748][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:54.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:54.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.753][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 14:04:54.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:54.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.770][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:54.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:54.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:54.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:54.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.860][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:54.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:54.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.864][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:54.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:54.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.868][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:54.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:54.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.871][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:54.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:54.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.877][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:54.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:54.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:54.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:54.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.905][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:54.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:54.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:54.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:54.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:54.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:54.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:54.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:54.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:54.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:54.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:54.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:54.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:54.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:54.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:54.930][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-10-17 14:04:54.933][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 14:04:54.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 14:04:54.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.937][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 14:04:54.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 14:04:54.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.940][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-17 14:04:54.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-17 14:04:54.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.943][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-17 14:04:54.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-17 14:04:54.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:54.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:54.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:54.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:54.988][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:54.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:54.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.025][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:55.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:55.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.037][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:55.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:55.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.040][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:55.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:55.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.067][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.068][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.070][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.097][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.101][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.104][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.108][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.109][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.110][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.111][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.124][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:55.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:55.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.128][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:55.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:55.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.131][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:55.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:55.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.135][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:55.135][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:55.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.137][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.138][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:55.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:55.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.149][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:55.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:55.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.154][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:55.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:55.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.156][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:55.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:55.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.159][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:55.159][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:55.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.161][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.161][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:55.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:55.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:55.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:55.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:55.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:55.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:55.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:55.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.202][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:55.203][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:55.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.205][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:55.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:55.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.227][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:55.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:55.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.231][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:55.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:55.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.235][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:55.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:55.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.239][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:55.240][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:55.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.241][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.242][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:55.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:55.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.254][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.255][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.257][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.262][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:55.263][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:55.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.265][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.270][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:55.271][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:55.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.273][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.278][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:55.295][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:55.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.302][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.308][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.309][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.310][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.319][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:55.320][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:55.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.321][ef$get] fields variable is a list.
biodb.INFO [2024-10-17 14:04:55.326][biodb::testThat]
biodb.INFO [2024-10-17 14:04:55.326][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-10-17 14:04:55.327][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:55.327][biodb::testThat]
biodb.DEBUG[2024-10-17 14:04:55.341][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-10-17 14:04:55.348][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:04:55.353][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-10-17 14:04:55.355][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:55.358][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-10-17 14:04:55.359][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:04:55.383][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:04:55.395][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-17 14:04:55.400][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:55.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:55.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:55.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:55.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:55.419][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:55.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:55.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:55.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:55.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:55.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:55.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.450][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:55.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:04:55.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.453][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:55.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:55.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.455][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:55.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:55.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.457][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:55.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:04:55.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.460][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:55.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:55.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.464][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:55.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:04:55.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.466][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 14:04:55.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:55.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.468][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 14:04:55.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:55.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.471][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:55.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:55.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.473][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:55.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:55.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.494][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.497][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.500][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 14:04:55.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.505][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-17 14:04:55.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.507][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.509][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.513][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 14:04:55.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.515][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.517][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.524][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.525][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:55.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:55.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.531][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:55.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:55.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.535][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:55.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:04:55.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:55.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:55.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:55.564][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-10-17 14:04:55.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-17 14:04:55.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-17 14:04:55.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-17 14:04:55.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-17 14:04:55.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-17 14:04:55.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-17 14:04:55.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 14:04:55.609][biodb::testThat]
biodb.INFO [2024-10-17 14:04:55.610][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-10-17 14:04:55.610][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:55.611][biodb::testThat]
biodb.TRACE[2024-10-17 14:04:55.613][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.614][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.615][ef$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:55.616][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-10-17 14:04:55.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:55.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:55.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:55.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:55.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:55.655][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-17 14:04:55.662][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-17 14:04:55.701][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:04:55.702][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:04:55.704][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-10-17 14:04:55.961][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-10-17 14:04:56.089][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:04:56.091][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-10-17 14:04:56.106][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-10-17 14:04:56.109][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-10-17 14:04:56.146][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:56.149][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:56.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:56.152][ef$get] fields variable is a list.
biodb.INFO [2024-10-17 14:04:56.162][biodb::testThat]
biodb.INFO [2024-10-17 14:04:56.165][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-10-17 14:04:56.166][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:56.168][biodb::testThat]
biodb.TRACE[2024-10-17 14:04:56.223][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:56.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:56.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:56.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:56.229][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:56.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:56.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:56.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:56.234][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:56.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:56.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:56.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:56.344][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-17 14:04:56.348][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:56.364][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-10-17 14:04:56.365][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:56.367][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-10-17 14:04:56.382][biodb::testThat]
biodb.INFO [2024-10-17 14:04:56.383][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-10-17 14:04:56.383][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:56.385][biodb::testThat]
biodb.TRACE[2024-10-17 14:04:56.406][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 14:04:56.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 14:04:56.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:56.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:56.410][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 14:04:56.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 14:04:56.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:56.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:56.424][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-17 14:04:56.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-17 14:04:56.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:56.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:56.426][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-17 14:04:56.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-17 14:04:56.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:56.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:56.475][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 14:04:56.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 14:04:56.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:56.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:56.484][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 14:04:56.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 14:04:56.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:56.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:56.489][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-17 14:04:56.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-17 14:04:56.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:56.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:56.491][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-17 14:04:56.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-17 14:04:56.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:56.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 14:04:56.501][biodb::testThat]
biodb.INFO [2024-10-17 14:04:56.503][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-10-17 14:04:56.504][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:56.505][biodb::testThat]
biodb.INFO [2024-10-17 14:04:56.515][biodb::testThat]
biodb.INFO [2024-10-17 14:04:56.516][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-10-17 14:04:56.517][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:56.518][biodb::testThat]
biodb.INFO [2024-10-17 14:04:56.527][biodb::testThat]
biodb.INFO [2024-10-17 14:04:56.528][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-10-17 14:04:56.529][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:56.530][biodb::testThat]
biodb.DEBUG[2024-10-17 14:04:56.534][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-10-17 14:04:56.646][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-10-17 14:04:56.755][biodb::testThat]
biodb.INFO [2024-10-17 14:04:56.756][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-10-17 14:04:56.759][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:56.760][biodb::testThat]
biodb.TRACE[2024-10-17 14:04:56.767][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:56.768][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:56.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:56.769][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:56.769][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:56.770][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:56.770][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:56.771][ef$get] fields variable is a list.
biodb.INFO [2024-10-17 14:04:56.774][biodb::testThat]
biodb.INFO [2024-10-17 14:04:56.775][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-10-17 14:04:56.776][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:56.777][biodb::testThat]
biodb.TRACE[2024-10-17 14:04:56.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:56.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:56.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:56.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:56.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:56.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:56.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:56.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:56.800][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:56.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:56.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:56.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:56.913][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-17 14:04:56.919][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:56.922][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-10-17 14:04:56.924][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:56.925][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-10-17 14:04:56.983][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-17 14:04:56.987][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:56.988][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-10-17 14:04:56.990][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:56.991][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-10-17 14:04:57.035][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:57.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:57.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:57.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:57.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:57.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:57.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:57.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:57.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:57.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:57.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:57.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:57.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:57.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:57.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:57.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:57.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:57.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:57.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:57.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:57.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:57.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:57.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:57.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:57.059][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:57.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:57.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:57.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:57.069][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-10-17 14:04:57.084][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:04:57.086][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:04:57.102][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-10-17 14:04:57.366][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-10-17 14:04:58.751][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:04:58.754][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-10-17 14:04:58.763][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-10-17 14:05:00.053][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-10-17 14:05:00.056][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:00.057][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:05:00.060][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-10-17 14:05:00.191][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-10-17 14:05:00.317][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:05:00.319][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-10-17 14:05:00.322][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-10-17 14:05:00.358][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-10-17 14:05:00.366][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:00.366][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:00.367][rule$waitAsNeeded] Wait 0.691968 second(s).
biodb.TRACE[2024-10-17 14:05:01.160][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-10-17 14:05:01.279][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-10-17 14:05:01.398][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:05:01.401][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-10-17 14:05:01.403][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-10-17 14:05:01.410][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-17 14:05:01.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-17 14:05:01.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:01.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 14:05:01.415][biodb::testThat]
biodb.INFO [2024-10-17 14:05:01.416][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-10-17 14:05:01.427][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:05:01.428][biodb::testThat]
biodb.TRACE[2024-10-17 14:05:01.431][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:05:01.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:05:01.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:01.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:01.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:05:01.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:05:01.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:01.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:01.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:01.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:01.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:01.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:01.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:01.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:01.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:01.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:01.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:01.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:01.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:01.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:01.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:01.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:01.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:01.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:05:01.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:01.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:01.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:01.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:01.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:01.462][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:01.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:01.464][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-10-17 14:05:01.466][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:01.467][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:01.468][rule$waitAsNeeded] Wait 0.691712 second(s).
biodb.TRACE[2024-10-17 14:05:02.314][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-10-17 14:05:02.582][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-10-17 14:05:03.648][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:05:03.650][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-10-17 14:05:03.658][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-10-17 14:05:04.816][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-10-17 14:05:04.862][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-10-17 14:05:04.864][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-10-17 14:05:04.865][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-10-17 14:05:04.866][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:05:04.867][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:05:04.868][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-17 14:05:04.869][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:05:04.870][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:05:04.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:04.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:04.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:04.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:04.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:04.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:04.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:04.904][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-10-17 14:05:04.908][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:04.909][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:05:04.911][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-10-17 14:05:05.005][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-10-17 14:05:05.093][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:05:05.096][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-10-17 14:05:05.099][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-10-17 14:05:05.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:05.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:05.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:05.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:05.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:05.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:05.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:05.114][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-10-17 14:05:05.117][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:05.118][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:05.119][rule$waitAsNeeded] Wait 0.791812 second(s).
biodb.TRACE[2024-10-17 14:05:06.062][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-10-17 14:05:06.149][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-10-17 14:05:06.241][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:05:06.248][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-10-17 14:05:06.256][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-10-17 14:05:06.268][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-10-17 14:05:06.271][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:05:06.272][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-10-17 14:05:06.274][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-17 14:05:06.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:06.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:06.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:06.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:06.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:06.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:06.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:05:06.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:06.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:06.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:06.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:06.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:06.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:06.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:06.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:06.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.307][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:05:06.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:05:06.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.311][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:05:06.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:05:06.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.316][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:06.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:06.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.321][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:06.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:06.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.327][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:06.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:06.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.332][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:06.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:06.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.337][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 14:05:06.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:06.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.343][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 14:05:06.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:06.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.348][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:06.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:06.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.351][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:06.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:06.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.355][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:06.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:06.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.359][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:06.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:06.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.381][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 14:05:06.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:06.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.388][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-17 14:05:06.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:06.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.392][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:06.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:06.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.397][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:06.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:06.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.403][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 14:05:06.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:06.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.407][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.411][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:06.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:06.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.419][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:06.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:06.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:06.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:06.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:06.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:06.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:05:06.436][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:06.437][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:06.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:06.444][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:06.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:06.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:06.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:05:06.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:06.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:06.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:06.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:06.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:06.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:06.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.468][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:05:06.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:05:06.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.473][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:05:06.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:05:06.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.477][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:06.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:06.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.496][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:06.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:06.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.530][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:06.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:06.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.533][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:06.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:06.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.535][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 14:05:06.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:06.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.538][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 14:05:06.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:06.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.541][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:06.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:06.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.544][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:06.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:06.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.547][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:06.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:06.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.550][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:06.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:06.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.553][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 14:05:06.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:06.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.558][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-17 14:05:06.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:06.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.561][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:06.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:06.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.565][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:06.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:06.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.568][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 14:05:06.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:06.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.574][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.579][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:06.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:06.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.587][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:06.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:06.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:06.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:06.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:06.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:06.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:06.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:06.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:06.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:06.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:06.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:06.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:06.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:06.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:06.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:06.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:06.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:06.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:05:06.638][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-10-17 14:05:06.648][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 14:05:06.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:06.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:06.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:06.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:06.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:06.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:06.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:05:06.667][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.671][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.674][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:06.675][private$selectFields]
biodb.TRACE[2024-10-17 14:05:06.675][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:05:06.676][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:05:06.677][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:06.678][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.679][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.680][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.680][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.681][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.682][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.684][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.685][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:06.685][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:06.686][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.687][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.688][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.689][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-17 14:05:06.690][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.693][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.697][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.711][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-10-17 14:05:06.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:06.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:06.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:06.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:06.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:06.729][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:06.730][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.TRACE[2024-10-17 14:05:06.732][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.736][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.739][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:06.740][private$selectFields]
biodb.TRACE[2024-10-17 14:05:06.741][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:05:06.742][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:05:06.742][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:06.743][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.744][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.746][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.747][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.748][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.750][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.751][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:06.751][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:06.752][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.753][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.755][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.756][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-17 14:05:06.757][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.760][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.764][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.768][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-10-17 14:05:06.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:06.770][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:06.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:06.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:06.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:06.779][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:06.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:05:06.782][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.789][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.807][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:06.808][private$selectFields]
biodb.TRACE[2024-10-17 14:05:06.809][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:05:06.809][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:05:06.811][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:06.813][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.814][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.816][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.817][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.818][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.819][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.820][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:06.821][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:06.822][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.823][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.824][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.825][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-17 14:05:06.827][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.830][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.835][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:06.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.841][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-10-17 14:05:06.842][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 14:05:06.844][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-17 14:05:06.860][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-17 14:05:06.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-17 14:05:06.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 14:05:06.870][biodb::testThat]
biodb.INFO [2024-10-17 14:05:06.872][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-10-17 14:05:06.873][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:05:06.874][biodb::testThat]
biodb.TRACE[2024-10-17 14:05:06.877][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:05:06.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:05:06.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:05:06.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:05:06.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:06.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:06.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:06.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:06.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:06.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:06.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:06.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:06.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:06.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:06.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:05:07.001][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:07.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:07.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:07.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:07.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:07.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:07.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:07.015][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-10-17 14:05:07.019][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:07.020][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:07.021][rule$waitAsNeeded] Wait 0.0403979 second(s).
biodb.TRACE[2024-10-17 14:05:07.214][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-10-17 14:05:07.497][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-10-17 14:05:08.858][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:05:08.861][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-10-17 14:05:08.871][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-10-17 14:05:10.495][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 14:05:10.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:10.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:10.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:10.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:10.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:10.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:10.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:05:10.542][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.546][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.569][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:10.570][private$selectFields]
biodb.TRACE[2024-10-17 14:05:10.571][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:05:10.572][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:05:10.573][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:10.574][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.575][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.576][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.577][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.578][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.579][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.580][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:10.591][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:10.592][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.593][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.595][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.596][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-17 14:05:10.597][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.601][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.604][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.608][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-10-17 14:05:10.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:10.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:10.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:10.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:10.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:10.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:10.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:05:10.621][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.626][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.630][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:10.631][private$selectFields]
biodb.TRACE[2024-10-17 14:05:10.632][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:05:10.632][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:05:10.633][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:10.634][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.635][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.637][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.638][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.639][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.641][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.642][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:10.643][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:10.644][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.645][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.647][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.648][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-17 14:05:10.649][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.653][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.657][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.661][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-10-17 14:05:10.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:10.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:10.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:10.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:10.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:10.672][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:10.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:05:10.674][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.678][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.682][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:10.683][private$selectFields]
biodb.TRACE[2024-10-17 14:05:10.684][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:05:10.685][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:05:10.686][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:10.687][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.688][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.690][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.691][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.692][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.695][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.696][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:10.697][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:10.698][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.699][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.701][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.702][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-17 14:05:10.703][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.706][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.710][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:10.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.714][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-10-17 14:05:10.715][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 14:05:10.716][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-17 14:05:10.727][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-17 14:05:10.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-17 14:05:10.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 14:05:10.736][biodb::testThat]
biodb.INFO [2024-10-17 14:05:10.737][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-10-17 14:05:10.738][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:05:10.739][biodb::testThat]
biodb.TRACE[2024-10-17 14:05:10.743][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:05:10.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:05:10.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:05:10.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:05:10.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:10.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:10.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.755][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:10.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:10.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:10.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:10.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:11.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:11.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:11.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:11.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:11.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:11.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:11.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:05:11.077][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:11.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:11.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:11.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:11.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:11.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:11.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:11.089][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-10-17 14:05:11.093][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:05:11.094][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-10-17 14:05:11.095][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:05:11.163][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-10-17 14:05:12.497][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 14:05:12.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:12.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:12.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:12.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:12.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:12.509][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:12.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:05:12.511][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.515][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.518][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:12.519][private$selectFields]
biodb.TRACE[2024-10-17 14:05:12.519][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:05:12.520][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:05:12.521][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:12.522][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.523][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.524][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.525][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.526][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.527][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.528][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.528][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:12.529][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:12.530][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.531][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.533][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.533][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-17 14:05:12.534][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.538][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.541][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.546][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-10-17 14:05:12.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:12.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:12.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:12.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:12.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:12.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:12.559][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.TRACE[2024-10-17 14:05:12.560][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.563][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.567][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:12.567][private$selectFields]
biodb.TRACE[2024-10-17 14:05:12.568][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:05:12.569][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:05:12.570][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:12.570][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.571][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.573][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.574][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.574][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.576][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.577][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:12.578][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:12.578][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.579][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.581][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.581][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-17 14:05:12.582][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.585][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.589][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.592][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-10-17 14:05:12.593][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:12.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:12.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:12.600][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:12.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:12.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:12.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:05:12.604][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.607][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.610][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:12.611][private$selectFields]
biodb.TRACE[2024-10-17 14:05:12.612][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:05:12.613][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:05:12.613][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:12.614][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.615][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.616][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.617][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.618][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.618][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.620][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.621][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:12.622][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:12.622][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.623][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.625][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.626][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-17 14:05:12.627][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.630][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.634][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:12.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:12.638][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-10-17 14:05:12.639][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 14:05:12.640][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-17 14:05:12.665][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-17 14:05:12.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-17 14:05:12.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:12.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 14:05:12.674][biodb::testThat]
biodb.INFO [2024-10-17 14:05:12.675][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-10-17 14:05:12.676][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:05:12.677][biodb::testThat]
biodb.DEBUG[2024-10-17 14:05:12.679][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-10-17 14:05:12.681][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:05:12.682][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.INFO [2024-10-17 14:05:12.684][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-10-17 14:05:12.685][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:05:12.686][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:05:12.687][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:05:12.688][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-17 14:05:12.689][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:05:12.690][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:05:12.707][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:12.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:12.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:12.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:12.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:12.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:12.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:12.721][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-10-17 14:05:12.724][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:12.726][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:05:12.727][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 14:05:12.820][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:12.822][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:12.823][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:12.824][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 14:05:12.911][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:12.912][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:12.913][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:12.914][rule$waitAsNeeded] Wait 0.812746 second(s).
biodb.TRACE[2024-10-17 14:05:13.879][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 14:05:13.976][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:13.978][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:13.980][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:13.981][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 14:05:14.076][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:14.078][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:14.079][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:14.080][rule$waitAsNeeded] Wait 0.798265 second(s).
biodb.TRACE[2024-10-17 14:05:14.929][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 14:05:15.023][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:15.024][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:15.025][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:15.027][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 14:05:15.122][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:15.123][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:15.125][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:15.126][rule$waitAsNeeded] Wait 0.801858 second(s).
biodb.TRACE[2024-10-17 14:05:16.080][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 14:05:16.168][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:16.169][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:16.169][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:16.170][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 14:05:16.358][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:16.360][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:16.361][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:16.362][rule$waitAsNeeded] Wait 0.716984 second(s).
biodb.TRACE[2024-10-17 14:05:17.160][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 14:05:17.247][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:17.248][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:17.250][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:17.251][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 14:05:17.348][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:17.350][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:17.351][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:17.352][rule$waitAsNeeded] Wait 0.807198 second(s).
biodb.TRACE[2024-10-17 14:05:18.312][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 14:05:18.401][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:18.403][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:18.405][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:18.406][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 14:05:18.499][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:18.500][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:18.501][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:18.503][rule$waitAsNeeded] Wait 0.808337 second(s).
biodb.TRACE[2024-10-17 14:05:19.463][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 14:05:19.553][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:19.554][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:19.555][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:19.557][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 14:05:19.756][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:19.758][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:19.759][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:19.760][rule$waitAsNeeded] Wait 0.702349 second(s).
biodb.TRACE[2024-10-17 14:05:20.605][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 14:05:20.695][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:20.696][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:20.698][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:20.699][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 14:05:20.784][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:20.786][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:20.787][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:20.788][rule$waitAsNeeded] Wait 0.816321 second(s).
biodb.TRACE[2024-10-17 14:05:21.786][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 14:05:21.890][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:21.892][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:21.893][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:21.895][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 14:05:22.216][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:22.218][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:22.219][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:22.220][rule$waitAsNeeded] Wait 0.535926 second(s).
biodb.TRACE[2024-10-17 14:05:22.901][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 14:05:22.994][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:22.995][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:22.996][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:22.997][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 14:05:23.082][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-10-17 14:05:23.085][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-10-17 14:05:23.087][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:05:23.088][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:05:23.089][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-17 14:05:23.091][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:23.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:23.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:23.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:23.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:23.099][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:23.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:05:23.102][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:23.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:23.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:23.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:23.105][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:23.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:23.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:23.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:23.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:23.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:23.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:23.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:23.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:23.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:23.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:23.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:23.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:23.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:23.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:23.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:23.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:23.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:23.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:23.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:23.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:23.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:23.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:23.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:23.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:23.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:23.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:23.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:05:23.128][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-10-17 14:05:23.129][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-10-17 14:05:23.138][biodb::testThat]
biodb.INFO [2024-10-17 14:05:23.139][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-10-17 14:05:23.140][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:05:23.141][biodb::testThat]
biodb.DEBUG[2024-10-17 14:05:23.150][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-10-17 14:05:23.151][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-10-17 14:05:23.152][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-10-17 14:05:23.153][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-10-17 14:05:23.155][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-10-17 14:05:23.156][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:05:23.157][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:05:23.157][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-17 14:05:23.158][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:05:23.159][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:05:23.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:23.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:23.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:23.170][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:23.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:23.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:23.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:23.174][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-10-17 14:05:23.177][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:23.178][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:23.179][rule$waitAsNeeded] Wait 0.721604 second(s).
biodb.TRACE[2024-10-17 14:05:24.052][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 14:05:24.136][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:24.138][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:24.139][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:24.140][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 14:05:24.230][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:24.231][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:24.232][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:24.233][rule$waitAsNeeded] Wait 0.818079 second(s).
biodb.TRACE[2024-10-17 14:05:25.203][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 14:05:25.300][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:25.301][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:25.302][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:25.303][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 14:05:25.388][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:25.389][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:25.390][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:25.391][rule$waitAsNeeded] Wait 0.811374 second(s).
biodb.TRACE[2024-10-17 14:05:26.349][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 14:05:26.441][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:26.443][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:26.444][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:26.445][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 14:05:26.535][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:26.536][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:26.538][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:26.539][rule$waitAsNeeded] Wait 0.809406 second(s).
biodb.TRACE[2024-10-17 14:05:27.500][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 14:05:27.592][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:27.593][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:27.594][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:27.595][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 14:05:27.686][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:27.687][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:27.688][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:27.689][rule$waitAsNeeded] Wait 0.810581 second(s).
biodb.TRACE[2024-10-17 14:05:28.651][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 14:05:28.744][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:28.746][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:28.748][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:28.749][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 14:05:29.084][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:29.085][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:29.086][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:29.087][rule$waitAsNeeded] Wait 0.563485 second(s).
biodb.TRACE[2024-10-17 14:05:29.802][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 14:05:29.888][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:29.889][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:29.890][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:29.891][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 14:05:30.146][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:30.147][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:30.148][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:30.149][rule$waitAsNeeded] Wait 0.652873 second(s).
biodb.TRACE[2024-10-17 14:05:30.954][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 14:05:31.045][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:31.046][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:31.047][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:31.048][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 14:05:31.396][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:31.398][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:31.399][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:31.400][rule$waitAsNeeded] Wait 0.553104 second(s).
biodb.TRACE[2024-10-17 14:05:32.105][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 14:05:32.189][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:32.190][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:32.191][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:32.192][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 14:05:32.285][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:32.286][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:32.287][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:32.288][rule$waitAsNeeded] Wait 0.815713 second(s).
biodb.TRACE[2024-10-17 14:05:33.256][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 14:05:33.350][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:33.351][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:33.352][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:33.353][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 14:05:33.445][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:33.446][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:33.447][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:33.448][rule$waitAsNeeded] Wait 0.80683 second(s).
biodb.TRACE[2024-10-17 14:05:34.376][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 14:05:34.474][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 14:05:34.475][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 14:05:34.476][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 14:05:34.477][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 14:05:34.561][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 14:05:34.562][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:34.563][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:34.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:34.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:34.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:34.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:34.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:34.573][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-10-17 14:05:34.576][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:34.577][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:34.579][rule$waitAsNeeded] Wait 0.796794 second(s).
biodb.TRACE[2024-10-17 14:05:35.527][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-10-17 14:05:35.614][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2024-10-17 14:05:35.709][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:05:35.711][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2024-10-17 14:05:35.715][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2024-10-17 14:05:35.718][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-10-17 14:05:35.720][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:05:35.721][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-10-17 14:05:35.722][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-17 14:05:35.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:35.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:35.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:35.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:35.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:35.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:35.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:05:35.736][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:35.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:35.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.739][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:35.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:35.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:35.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:35.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:05:35.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:35.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:35.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:35.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:35.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:35.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:35.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:05:35.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:35.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:35.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:35.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:35.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:35.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:35.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.774][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:35.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:35.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.778][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:05:35.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:05:35.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.781][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:05:35.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:05:35.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.785][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:05:35.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:05:35.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.788][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:05:35.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:05:35.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.830][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:35.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:35.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.833][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:35.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:35.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.837][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:35.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:35.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.840][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:35.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:35.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.843][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 14:05:35.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:35.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.847][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 14:05:35.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:35.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.850][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:35.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:35.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.854][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:35.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:35.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.857][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:35.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:35.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.860][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:35.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:35.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.864][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 14:05:35.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:35.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.868][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-17 14:05:35.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:35.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.872][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:35.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:35.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:35.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:35.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.878][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 14:05:35.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:35.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.883][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:35.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:35.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.887][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:35.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:35.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.890][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:35.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:35.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.893][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:35.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:35.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.897][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:35.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:35.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.900][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:35.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:35.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.904][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:35.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:35.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:35.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:35.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.911][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:35.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:35.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:35.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:35.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:35.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:35.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:35.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:35.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:35.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:35.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:35.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:35.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:35.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:35.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:35.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:35.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:35.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:35.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:35.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:35.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:35.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:35.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:35.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:35.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:35.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:35.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:05:35.951][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2024-10-17 14:05:35.951][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-10-17 14:05:35.952][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-10-17 14:05:35.966][biodb::testThat]
biodb.INFO [2024-10-17 14:05:35.967][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-10-17 14:05:35.968][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:05:35.968][biodb::testThat]
biodb.INFO [2024-10-17 14:05:35.992][biodb::testThat]
biodb.INFO [2024-10-17 14:05:35.993][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-10-17 14:05:35.994][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:05:35.995][biodb::testThat]
biodb.INFO [2024-10-17 14:05:36.003][biodb::testThat]
biodb.INFO [2024-10-17 14:05:36.004][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-10-17 14:05:36.005][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:05:36.005][biodb::testThat]
biodb.DEBUG[2024-10-17 14:05:36.009][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-10-17 14:05:36.012][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:36.014][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:36.015][rule$waitAsNeeded] Wait 0.511617 second(s).
biodb.TRACE[2024-10-17 14:05:36.678][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-10-17 14:05:36.936][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-10-17 14:05:38.037][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:05:38.039][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-10-17 14:05:38.050][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-10-17 14:05:39.258][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:39.260][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:39.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:39.262][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:39.263][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:39.264][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:39.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:39.266][ef$get] fields variable is a list.
biodb.INFO [2024-10-17 14:05:39.268][biodb::testThat]
biodb.INFO [2024-10-17 14:05:39.269][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-10-17 14:05:39.270][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:05:39.271][biodb::testThat]
biodb.ERROR[2024-10-17 14:05:39.285][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-10-17 14:05:39.305][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-10-17 14:05:39.321][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 14:05:39.322][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-10-17 14:05:39.323][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-10-17 14:05:39.324][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 14:05:39.326][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:39.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:39.327][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.329][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-17 14:05:39.342][biodb::testContext]
biodb.INFO [2024-10-17 14:05:39.343][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:05:39.344][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-10-17 14:05:39.345][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:05:39.346][biodb::testContext]
biodb.INFO [2024-10-17 14:05:39.348][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:05:39.351][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 14:05:39.356][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:05:39.358][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 14:05:39.359][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 14:05:39.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.362][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 14:05:39.363][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 14:05:39.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.367][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 14:05:39.368][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 14:05:39.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.371][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 14:05:39.372][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 14:05:39.373][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 14:05:39.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.376][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 14:05:39.377][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 14:05:39.378][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 14:05:39.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.381][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 14:05:39.382][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 14:05:39.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.384][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 14:05:39.385][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 14:05:39.386][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 14:05:39.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.389][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 14:05:39.390][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 14:05:39.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.394][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 14:05:39.395][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 14:05:39.396][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 14:05:39.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.399][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:05:39.400][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 14:05:39.401][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 14:05:39.402][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 14:05:39.403][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 14:05:39.403][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 14:05:39.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.406][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 14:05:39.407][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 14:05:39.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.410][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 14:05:39.411][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 14:05:39.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.414][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 14:05:39.415][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 14:05:39.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.419][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 14:05:39.420][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 14:05:39.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.423][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 14:05:39.424][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 14:05:39.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.428][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:05:39.428][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 14:05:39.446][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 14:05:39.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.450][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 14:05:39.451][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 14:05:39.452][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 14:05:39.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.455][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 14:05:39.457][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:39.458][self$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[2024-10-17 14:05:39.459][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.460][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:05:39.461][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.461][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:05:39.462][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:39.463][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:05:39.464][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:05:39.465][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:05:39.465][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.466][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 14:05:39.467][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:05:39.468][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:39.469][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.470][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:05:39.470][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:05:39.470][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:05:39.470][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:05:39.470][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:05:39.471][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:05:39.472][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:39.473][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:39.473][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:05:39.474][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:39.475][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:39.476][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:05:39.476][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:39.478][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:05:39.479][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:05:39.480][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:39.481][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:39.482][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 14:05:39.483][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:39.484][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:05:39.485][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.486][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:05:39.487][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.488][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:05:39.489][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:39.490][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:05:39.491][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:05:39.492][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:05:39.493][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.494][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 14:05:39.495][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:05:39.496][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:39.497][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.498][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:05:39.498][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:05:39.498][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:05:39.498][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:05:39.498][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:05:39.499][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:05:39.500][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:39.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:39.502][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:05:39.503][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:39.504][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:39.505][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:05:39.506][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:39.506][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:05:39.507][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:05:39.508][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:39.509][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:39.510][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 14:05:39.512][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.513][self$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[2024-10-17 14:05:39.514][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.515][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:05:39.516][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.517][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:05:39.518][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:39.519][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:05:39.520][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:05:39.521][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:05:39.522][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:39.523][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 14:05:39.524][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:05:39.525][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:39.526][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.527][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:39.527][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:05:39.528][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:39.529][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:39.530][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:05:39.531][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:39.532][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:39.532][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:05:39.533][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:39.534][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:05:39.536][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:05:39.536][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:39.537][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:39.538][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 14:05:39.540][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.541][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:05:39.542][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.543][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:05:39.544][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.544][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:05:39.545][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:39.546][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:05:39.547][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:05:39.548][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:05:39.549][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:39.549][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 14:05:39.550][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:05:39.551][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:39.552][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.553][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:39.554][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:05:39.555][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:39.556][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:39.557][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:05:39.557][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:39.558][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:39.559][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:05:39.560][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:39.561][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:05:39.561][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:05:39.562][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:39.563][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:39.564][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:05:39.565][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.594][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[2024-10-17 14:05:39.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.598][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[2024-10-17 14:05:39.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.602][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[2024-10-17 14:05:39.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.609][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[2024-10-17 14:05:39.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.612][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[2024-10-17 14:05:39.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.616][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[2024-10-17 14:05:39.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.623][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.DEBUG[2024-10-17 14:05:39.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.627][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[2024-10-17 14:05:39.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.634][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.DEBUG[2024-10-17 14:05:39.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.641][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 14:05:39.641][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 14:05:39.642][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 14:05:39.643][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 14:05:39.644][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 14:05:39.645][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 14:05:39.647][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 14:05:39.648][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 14:05:39.649][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 14:05:39.649][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 14:05:39.650][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 14:05:39.650][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 14:05:39.651][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 14:05:39.651][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 14:05:39.652][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 14:05:39.654][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 14:05:39.655][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 14:05:39.656][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 14:05:39.657][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 14:05:39.658][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 14:05:39.660][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 14:05:39.661][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 14:05:39.662][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 14:05:39.663][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 14:05:39.665][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 14:05:39.666][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 14:05:39.667][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 14:05:39.669][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 14:05:39.670][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 14:05:39.671][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 14:05:39.671][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 14:05:39.673][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 14:05:39.674][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 14:05:39.675][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 14:05:39.676][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 14:05:39.678][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 14:05:39.679][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 14:05:39.680][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 14:05:39.681][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 14:05:39.682][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 14:05:39.683][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 14:05:39.685][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 14:05:39.686][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 14:05:39.687][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 14:05:39.688][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 14:05:39.689][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 14:05:39.690][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 14:05:39.691][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 14:05:39.691][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 14:05:39.692][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 14:05:39.692][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 14:05:39.693][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 14:05:39.693][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 14:05:39.693][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 14:05:39.694][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 14:05:39.694][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 14:05:39.695][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 14:05:39.695][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 14:05:39.696][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 14:05:39.696][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 14:05:39.697][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 14:05:39.697][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 14:05:39.698][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 14:05:39.698][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 14:05:39.699][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 14:05:39.699][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 14:05:39.699][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 14:05:39.700][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 14:05:39.700][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 14:05:39.701][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 14:05:39.702][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 14:05:39.702][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 14:05:39.703][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 14:05:39.703][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 14:05:39.704][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 14:05:39.704][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 14:05:39.705][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 14:05:39.705][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 14:05:39.706][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 14:05:39.706][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 14:05:39.707][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 14:05:39.707][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 14:05:39.708][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 14:05:39.708][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 14:05:39.710][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:05:39.710][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:05:39.711][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.713][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:39.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:39.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:39.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:39.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.721][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[2024-10-17 14:05:39.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:39.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:39.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.726][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[2024-10-17 14:05:39.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:39.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:39.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:39.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:39.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.733][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[2024-10-17 14:05:39.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:39.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:39.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.736][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[2024-10-17 14:05:39.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:39.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:39.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.738][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[2024-10-17 14:05:39.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:39.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:39.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:39.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:39.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.747][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[2024-10-17 14:05:39.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:39.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:39.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.749][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[2024-10-17 14:05:39.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:39.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:39.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.754][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[2024-10-17 14:05:39.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:39.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:39.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:39.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:39.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:39.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:39.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:39.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:39.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:39.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:39.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:39.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:39.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:39.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:39.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:39.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:39.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:39.798][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-10-17 14:05:39.799][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-10-17 14:05:39.801][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:39.802][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 14:05:39.803][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.804][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:05:39.804][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.805][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:05:39.806][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.807][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:05:39.807][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:05:39.808][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:05:39.809][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.810][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-10-17 14:05:39.811][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:05:39.811][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-10-17 14:05:39.811][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-10-17 14:05:39.811][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-10-17 14:05:39.811][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-10-17 14:05:39.811][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-10-17 14:05:39.811][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-10-17 14:05:39.811][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-10-17 14:05:39.811][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-10-17 14:05:39.811][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-10-17 14:05:39.812][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:39.812][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:05:39.812][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:05:39.812][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:05:39.813][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:39.813][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:39.813][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:05:39.814][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:39.814][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:39.814][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:05:39.815][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-17 14:05:39.815][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-10-17 14:05:39.815][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:05:39.815][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:05:39.815][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:39.816][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:39.816][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-10-17 14:05:39.817][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 14:05:39.819][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-10-17 14:05:39.821][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-10-17 14:05:39.822][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-10-17 14:05:39.823][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-10-17 14:05:39.824][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-17 14:05:39.825][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-17 14:05:39.826][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-10-17 14:05:39.827][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-10-17 14:05:39.828][biodb::testThat]
biodb.INFO [2024-10-17 14:05:39.828][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-10-17 14:05:39.829][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:05:39.829][biodb::testThat]
biodb.DEBUG[2024-10-17 14:05:39.832][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-10-17 14:05:39.836][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:39.837][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:05:39.839][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-10-17 14:05:39.959][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-10-17 14:05:40.081][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:05:40.083][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-10-17 14:05:40.085][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-10-17 14:05:40.092][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-10-17 14:05:40.095][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:40.096][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:40.098][rule$waitAsNeeded] Wait 0.740849 second(s).
biodb.TRACE[2024-10-17 14:05:40.991][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-10-17 14:05:41.113][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-10-17 14:05:41.240][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:05:41.243][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-10-17 14:05:41.248][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-10-17 14:05:41.261][biodb::testThat]
biodb.INFO [2024-10-17 14:05:41.262][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-10-17 14:05:41.263][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:05:41.264][biodb::testThat]
biodb.INFO [2024-10-17 14:05:41.294][biodb::testThat]
biodb.INFO [2024-10-17 14:05:41.295][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-10-17 14:05:41.296][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:05:41.297][biodb::testThat]
biodb.DEBUG[2024-10-17 14:05:41.300][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-10-17 14:05:41.304][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:41.305][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:41.306][rule$waitAsNeeded] Wait 0.683645 second(s).
biodb.TRACE[2024-10-17 14:05:42.142][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-10-17 14:05:42.228][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-10-17 14:05:42.314][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:05:42.316][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-10-17 14:05:42.321][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-10-17 14:05:42.327][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-10-17 14:05:42.330][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:05:42.331][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-10-17 14:05:42.332][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:05:42.334][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-10-17 14:05:42.340][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-10-17 14:05:42.343][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:42.344][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:42.345][rule$waitAsNeeded] Wait 0.795255 second(s).
biodb.TRACE[2024-10-17 14:05:43.293][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-10-17 14:05:43.378][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-10-17 14:05:43.457][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:05:43.459][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-10-17 14:05:43.464][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-10-17 14:05:43.471][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-10-17 14:05:43.475][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:43.476][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:43.477][rule$waitAsNeeded] Wait 0.81458 second(s).
biodb.TRACE[2024-10-17 14:05:44.444][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-10-17 14:05:44.694][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-10-17 14:05:45.142][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:05:45.144][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-10-17 14:05:45.149][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-10-17 14:05:45.272][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-10-17 14:05:45.275][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:45.276][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:45.278][rule$waitAsNeeded] Wait 0.165394 second(s).
biodb.TRACE[2024-10-17 14:05:45.492][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-10-17 14:05:45.748][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-10-17 14:05:46.217][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:05:46.220][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-10-17 14:05:46.225][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-10-17 14:05:46.418][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 14:05:46.420][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-10-17 14:05:46.422][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-10-17 14:05:46.422][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 14:05:46.423][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:46.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:46.425][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.427][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-17 14:05:46.432][biodb::testContext]
biodb.INFO [2024-10-17 14:05:46.433][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:05:46.434][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-10-17 14:05:46.435][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:05:46.436][biodb::testContext]
biodb.INFO [2024-10-17 14:05:46.438][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:05:46.440][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 14:05:46.445][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:05:46.446][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 14:05:46.447][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 14:05:46.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.450][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 14:05:46.451][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 14:05:46.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.454][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 14:05:46.454][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 14:05:46.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.457][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 14:05:46.458][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 14:05:46.459][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 14:05:46.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.462][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 14:05:46.463][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 14:05:46.463][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 14:05:46.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.467][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 14:05:46.468][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 14:05:46.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.472][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 14:05:46.473][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 14:05:46.474][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 14:05:46.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.477][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 14:05:46.478][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 14:05:46.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.481][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 14:05:46.482][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 14:05:46.483][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 14:05:46.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.485][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:05:46.486][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 14:05:46.487][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 14:05:46.488][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 14:05:46.489][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 14:05:46.489][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 14:05:46.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.492][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 14:05:46.493][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 14:05:46.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.497][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 14:05:46.498][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 14:05:46.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.501][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[2024-10-17 14:05:46.501][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 14:05:46.502][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 14:05:46.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.505][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 14:05:46.506][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 14:05:46.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.509][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 14:05:46.510][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 14:05:46.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.513][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:05:46.514][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 14:05:46.532][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 14:05:46.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.536][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 14:05:46.537][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 14:05:46.538][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 14:05:46.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.541][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 14:05:46.543][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:46.544][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-17 14:05:46.545][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.546][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:05:46.546][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.547][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:05:46.548][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:46.549][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:05:46.550][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:05:46.551][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:05:46.551][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.552][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 14:05:46.553][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:05:46.554][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:46.555][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.555][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:05:46.555][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:05:46.555][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:05:46.555][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:05:46.555][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:05:46.556][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:05:46.557][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:46.558][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:46.559][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:05:46.560][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:46.560][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:46.561][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:05:46.562][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:46.563][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:05:46.563][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:05:46.564][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:46.565][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:46.566][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 14:05:46.568][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:46.569][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:05:46.570][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.571][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:05:46.572][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.573][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:05:46.574][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:46.575][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:05:46.576][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:05:46.577][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:05:46.577][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.578][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 14:05:46.579][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:05:46.580][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:46.581][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.582][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:05:46.582][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:05:46.582][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:05:46.582][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:05:46.582][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:05:46.583][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:05:46.583][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:46.585][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:46.586][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:05:46.587][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:46.588][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:46.589][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:05:46.589][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:46.590][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:05:46.591][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:05:46.592][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:46.593][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:46.594][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 14:05:46.595][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.597][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-17 14:05:46.598][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.599][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:05:46.599][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.600][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:05:46.601][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:46.602][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:05:46.603][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:05:46.604][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:05:46.604][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:46.605][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 14:05:46.606][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:05:46.608][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:46.609][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.610][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:46.610][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:05:46.611][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:46.612][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:46.613][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:05:46.614][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:46.614][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:46.615][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:05:46.616][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:46.617][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:05:46.618][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:05:46.618][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:46.619][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:46.620][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 14:05:46.622][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.623][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:05:46.624][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.625][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:05:46.626][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.626][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:05:46.627][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:46.628][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:05:46.629][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:05:46.630][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:05:46.630][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:46.631][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 14:05:46.632][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:05:46.633][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:46.634][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.635][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:46.636][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:05:46.637][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:46.638][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:46.639][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:05:46.640][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:46.641][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:46.641][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:05:46.642][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:46.643][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:05:46.644][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:05:46.644][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:46.645][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:46.646][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:05:46.647][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.652][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.DEBUG[2024-10-17 14:05:46.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.664][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[2024-10-17 14:05:46.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.668][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[2024-10-17 14:05:46.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.672][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[2024-10-17 14:05:46.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.675][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[2024-10-17 14:05:46.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.679][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[2024-10-17 14:05:46.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.724][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[2024-10-17 14:05:46.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.727][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[2024-10-17 14:05:46.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.732][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[2024-10-17 14:05:46.733][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 14:05:46.734][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 14:05:46.736][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 14:05:46.738][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 14:05:46.739][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 14:05:46.741][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 14:05:46.742][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 14:05:46.744][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 14:05:46.746][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 14:05:46.747][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 14:05:46.748][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 14:05:46.749][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 14:05:46.750][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 14:05:46.752][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 14:05:46.753][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 14:05:46.755][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 14:05:46.756][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 14:05:46.758][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 14:05:46.760][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 14:05:46.761][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 14:05:46.763][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 14:05:46.764][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 14:05:46.766][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 14:05:46.768][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 14:05:46.770][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 14:05:46.771][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 14:05:46.773][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 14:05:46.775][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 14:05:46.776][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 14:05:46.778][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 14:05:46.780][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 14:05:46.781][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 14:05:46.783][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 14:05:46.785][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 14:05:46.786][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 14:05:46.788][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 14:05:46.789][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 14:05:46.791][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 14:05:46.793][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 14:05:46.794][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 14:05:46.796][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 14:05:46.798][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 14:05:46.799][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 14:05:46.801][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 14:05:46.802][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 14:05:46.804][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 14:05:46.805][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 14:05:46.806][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 14:05:46.807][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 14:05:46.808][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 14:05:46.810][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 14:05:46.811][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 14:05:46.813][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 14:05:46.814][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 14:05:46.816][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 14:05:46.817][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 14:05:46.818][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 14:05:46.819][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 14:05:46.820][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 14:05:46.822][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 14:05:46.823][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 14:05:46.824][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 14:05:46.825][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 14:05:46.826][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 14:05:46.828][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 14:05:46.830][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 14:05:46.831][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 14:05:46.832][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 14:05:46.833][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 14:05:46.834][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 14:05:46.836][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 14:05:46.837][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 14:05:46.838][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 14:05:46.839][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 14:05:46.840][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 14:05:46.841][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 14:05:46.843][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 14:05:46.844][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 14:05:46.845][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 14:05:46.846][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 14:05:46.847][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 14:05:46.849][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 14:05:46.850][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 14:05:46.851][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 14:05:46.853][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:05:46.854][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:05:46.855][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.856][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:46.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:46.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:46.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:46.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.867][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.DEBUG[2024-10-17 14:05:46.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:46.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:46.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:46.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:46.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.878][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[2024-10-17 14:05:46.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:46.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:46.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.883][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[2024-10-17 14:05:46.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:46.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:46.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.888][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[2024-10-17 14:05:46.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:46.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:46.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.893][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[2024-10-17 14:05:46.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:46.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:46.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:46.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:46.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:46.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:46.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:46.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:46.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:46.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:46.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:46.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:46.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:46.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:46.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:46.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:46.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:46.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:46.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.941][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[2024-10-17 14:05:46.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:05:46.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:46.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:46.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:46.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:46.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:46.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:46.948][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-10-17 14:05:46.950][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-10-17 14:05:46.952][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:46.953][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 14:05:46.954][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.954][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:05:46.955][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.956][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:05:46.957][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.958][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:05:46.959][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:05:46.960][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:05:46.961][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.962][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-10-17 14:05:46.963][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:05:46.964][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-10-17 14:05:46.964][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-10-17 14:05:46.964][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-10-17 14:05:46.964][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-10-17 14:05:46.964][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-10-17 14:05:46.964][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-10-17 14:05:46.964][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-10-17 14:05:46.964][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-10-17 14:05:46.964][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-10-17 14:05:46.965][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 14:05:46.966][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:05:46.966][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:05:46.967][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:05:46.968][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:46.969][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:46.969][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:05:46.970][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:05:46.971][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:05:46.972][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:05:46.973][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-17 14:05:46.973][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-10-17 14:05:46.973][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:05:46.974][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:05:46.975][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 14:05:46.976][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:05:46.977][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-10-17 14:05:46.978][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 14:05:46.982][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-10-17 14:05:46.983][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-10-17 14:05:46.984][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-10-17 14:05:46.985][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-10-17 14:05:46.986][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-17 14:05:46.987][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-17 14:05:46.988][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-10-17 14:05:46.989][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-10-17 14:05:47.006][biodb::testThat]
biodb.INFO [2024-10-17 14:05:47.008][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-10-17 14:05:47.009][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:05:47.010][biodb::testThat]
biodb.DEBUG[2024-10-17 14:05:47.014][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-10-17 14:05:47.018][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:05:47.019][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-10-17 14:05:47.020][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:05:47.081][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-10-17 14:05:48.715][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-10-17 14:05:48.716][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-10-17 14:05:48.718][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-10-17 14:05:48.720][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-10-17 14:05:48.721][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:05:48.722][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:05:48.723][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-17 14:05:48.724][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:05:48.725][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:05:48.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:48.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:48.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:48.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:48.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:48.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:48.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:48.741][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2024-10-17 14:05:48.744][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:48.745][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:05:48.746][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-10-17 14:05:48.838][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.DEBUG[2024-10-17 14:05:48.925][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:05:48.927][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.content"
biodb.TRACE[2024-10-17 14:05:48.931][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.request"
biodb.DEBUG[2024-10-17 14:05:48.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:48.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:48.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:48.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:48.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:48.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:48.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:05:48.944][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-10-17 14:05:48.947][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:05:48.948][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:05:48.949][rule$waitAsNeeded] Wait 0.796355 second(s).
biodb.TRACE[2024-10-17 14:05:49.774][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-10-17 14:05:49.860][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-10-17 14:05:49.947][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:05:49.950][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-10-17 14:05:49.955][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.TRACE[2024-10-17 14:05:49.957][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv"
biodb.DEBUG[2024-10-17 14:05:49.959][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:05:49.960][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-10-17 14:05:49.961][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-17 14:05:49.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:49.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:49.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:49.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:49.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:49.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:49.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:05:49.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:49.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:49.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:49.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:49.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:49.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:49.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:49.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:49.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:49.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:49.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:49.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:49.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:49.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:49.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:49.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:49.994][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:05:49.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:05:49.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:49.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:49.997][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:05:49.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:05:49.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.001][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.004][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.008][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.011][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.014][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 14:05:50.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.019][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 14:05:50.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.023][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:50.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:50.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.026][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:50.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:50.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.030][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.034][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.038][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 14:05:50.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.042][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-17 14:05:50.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.045][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.049][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.052][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 14:05:50.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.056][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.060][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.063][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.067][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.072][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.076][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.079][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.086][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:05:50.101][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:50.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:50.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:50.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:50.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:50.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:50.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:05:50.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.125][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.130][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.134][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:05:50.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 14:05:50.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.138][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:05:50.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:05:50.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.142][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.146][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.150][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.154][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.158][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 14:05:50.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.162][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 14:05:50.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.167][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:50.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:50.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.171][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:50.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:50.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.175][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.178][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.182][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 14:05:50.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.186][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-17 14:05:50.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.234][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.239][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.243][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 14:05:50.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.246][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.250][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.256][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:05:50.310][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-10-17 14:05:50.313][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 14:05:50.314][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:50.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:50.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:50.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:50.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:50.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:50.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:05:50.327][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 14:05:50.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 14:05:50.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.330][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 14:05:50.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 14:05:50.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.334][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-17 14:05:50.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-17 14:05:50.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.337][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-17 14:05:50.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-17 14:05:50.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.340][private$selectFields] Fields none
biodb.TRACE[2024-10-17 14:05:50.341][private$selectFields]
biodb.TRACE[2024-10-17 14:05:50.342][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-10-17 14:05:50.343][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:05:50.343][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:50.344][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.345][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.347][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.347][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.348][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.350][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.350][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.351][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.353][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.354][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.354][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.356][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.357][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.358][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.358][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.359][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.360][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:50.361][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:50.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.363][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.364][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.364][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.367][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.368][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.369][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.370][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.370][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.371][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.372][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.373][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.374][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.375][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.375][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.377][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.378][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.379][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.380][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.381][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.382][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.383][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.384][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.384][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.385][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.387][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.388][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:50.388][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:50.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.391][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.392][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.393][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.395][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.395][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.396][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.398][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.399][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:50.400][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:50.401][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.402][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.403][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.404][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.405][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.406][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.407][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.408][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.409][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.410][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.411][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.412][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.414][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.414][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.415][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.418][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.419][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:50.420][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:50.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.421][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.422][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.423][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.425][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.425][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.426][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.429][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.430][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-10-17 14:05:50.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.453][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.456][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.459][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.463][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.466][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.469][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.483][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:50.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:50.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.486][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:50.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:50.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.490][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:50.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:50.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.497][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.501][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.506][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.509][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.512][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.524][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2024-10-17 14:05:50.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:05:50.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:50.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:50.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:50.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:50.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:50.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:05:50.553][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 14:05:50.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 14:05:50.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.556][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 14:05:50.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 14:05:50.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.560][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-17 14:05:50.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-17 14:05:50.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.564][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-17 14:05:50.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-17 14:05:50.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.567][private$selectFields] Fields none
biodb.TRACE[2024-10-17 14:05:50.567][private$selectFields]
biodb.TRACE[2024-10-17 14:05:50.568][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-10-17 14:05:50.569][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:05:50.570][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:50.570][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.571][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.573][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.574][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.574][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.576][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.577][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.577][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.579][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.580][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.581][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.582][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.583][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.584][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.585][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.586][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:50.587][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:50.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.588][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.589][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.590][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.591][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.592][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.593][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.595][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.596][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.597][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.598][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.599][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.600][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.601][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.603][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.604][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.605][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.606][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.606][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.607][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.608][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.610][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.611][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.612][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.614][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.615][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:50.616][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:50.616][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.617][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.618][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.619][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.620][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.620][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.621][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.622][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.623][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.624][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:50.625][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-17 14:05:50.626][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.627][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.628][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.629][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.630][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.631][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.632][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.633][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.634][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.634][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.635][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.636][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.638][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.639][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.640][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.641][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.642][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:50.643][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:50.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.644][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.645][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.646][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.647][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.648][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.649][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.650][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.650][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.651][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-10-17 14:05:50.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:05:50.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:05:50.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:05:50.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.672][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.675][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.679][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 14:05:50.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.682][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.685][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.688][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 14:05:50.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:05:50.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.701][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:50.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:50.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.704][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:50.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:50.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.708][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:05:50.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:05:50.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.711][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:05:50.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:05:50.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.721][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.724][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.727][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 14:05:50.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:05:50.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:05:50.734][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-10-17 14:05:50.735][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 14:05:50.736][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-10-17 14:05:50.742][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 14:05:50.744][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-10-17 14:05:50.746][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-10-17 14:05:50.747][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 14:05:50.748][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:05:50.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:05:50.749][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:05:50.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:05:50.751][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:05:50.751][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 170 ]
> 
> proc.time()
   user  system elapsed 
 21.304   2.106  59.645

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn2.0840.6653.096
LipidmapsStructureEntry0.2750.0150.301