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This page was generated on 2023-04-12 11:06:00 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for biodbLipidmaps on lconway


To the developers/maintainers of the biodbLipidmaps package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 184/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.4.1  (landing page)
Pierrick Roger
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_16
git_last_commit: 75afc75
git_last_commit_date: 2022-12-01 07:31:40 -0400 (Thu, 01 Dec 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: biodbLipidmaps
Version: 1.4.1
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_1.4.1.tar.gz
StartedAt: 2023-04-10 19:03:20 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 19:04:35 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 74.8 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_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.4.1’
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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/4.2/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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2023-04-10 19:04:08.733][biodb::testContext]
biodb.INFO [2023-04-10 19:04:08.756][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:04:08.757][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-04-10 19:04:08.759][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:04:08.760][biodb::testContext]
biodb.INFO [2023-04-10 19:04:08.768][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:04:08.771][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-04-10 19:04:08.778][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:04:08.779][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-10 19:04:08.780][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-10 19:04:08.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:08.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:08.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:08.784][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-10 19:04:08.803][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-10 19:04:08.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:08.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:08.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:08.807][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-10 19:04:08.808][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-10 19:04:08.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:08.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:08.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:08.812][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-10 19:04:08.813][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-10 19:04:08.814][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-10 19:04:08.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:08.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:08.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:08.818][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-10 19:04:08.819][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-10 19:04:08.820][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-10 19:04:08.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:08.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:08.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:08.823][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-10 19:04:08.824][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-10 19:04:08.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:08.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:08.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:08.828][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-10 19:04:08.829][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-10 19:04:08.830][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-10 19:04:08.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:08.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:08.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:08.834][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-10 19:04:08.835][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-10 19:04:08.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:08.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:08.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:08.839][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-10 19:04:08.840][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-10 19:04:08.841][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-10 19:04:08.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:08.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:08.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:08.845][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:04:08.846][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-10 19:04:08.847][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-10 19:04:08.848][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-10 19:04:08.849][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-10 19:04:08.850][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-10 19:04:08.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:08.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:08.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:08.853][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-10 19:04:08.854][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-10 19:04:08.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:08.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:08.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:08.858][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-10 19:04:08.859][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-10 19:04:08.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:08.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:08.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:08.862][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-10 19:04:08.863][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-10 19:04:08.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:08.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:08.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:08.866][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-10 19:04:08.867][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-10 19:04:08.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:08.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:08.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:08.870][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-10 19:04:08.871][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-10 19:04:08.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:08.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:08.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:08.875][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:04:08.876][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-10 19:04:08.902][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-10 19:04:08.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:08.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:08.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:08.908][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-10 19:04:08.910][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-10 19:04:08.911][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-10 19:04:08.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:08.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:08.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:08.919][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-10 19:04:08.986][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:09.007][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-10 19:04:09.009][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.010][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:04:09.012][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.013][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:04:09.014][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:09.016][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:04:09.017][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:04:09.019][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:04:09.020][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.021][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-10 19:04:09.022][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:04:09.023][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:09.025][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.026][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:04:09.026][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:04:09.026][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:04:09.026][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:04:09.026][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:04:09.027][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:04:09.028][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:09.030][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:09.031][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:04:09.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:09.033][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:09.034][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:04:09.035][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:09.036][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:04:09.037][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:04:09.038][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:09.039][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:09.041][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-10 19:04:09.043][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:09.044][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:04:09.046][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.047][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:04:09.048][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.050][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:04:09.051][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:09.052][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:04:09.053][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:04:09.054][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:04:09.056][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.056][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-10 19:04:09.057][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:04:09.058][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:09.059][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.061][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:04:09.061][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:04:09.061][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:04:09.061][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:04:09.061][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:04:09.062][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:04:09.063][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:09.064][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:09.065][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:04:09.067][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:09.068][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:09.069][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:04:09.070][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:09.071][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:04:09.072][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:04:09.073][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:09.073][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:09.074][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-10 19:04:09.076][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.078][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-10 19:04:09.079][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.080][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:04:09.082][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.083][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:04:09.084][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:09.085][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:04:09.087][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:04:09.088][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:04:09.089][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:09.091][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-10 19:04:09.092][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:04:09.093][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:09.095][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.096][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:09.097][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:04:09.098][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:09.099][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:09.101][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:04:09.101][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:09.102][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:09.103][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:04:09.105][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:09.106][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:04:09.107][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:04:09.108][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:09.109][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:09.111][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-10 19:04:09.113][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.114][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:04:09.116][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.117][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:04:09.118][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.119][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:04:09.120][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:09.122][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:04:09.123][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:04:09.124][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:04:09.125][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:09.126][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-10 19:04:09.127][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:04:09.128][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:09.130][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.131][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:09.132][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:04:09.133][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:09.134][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:09.136][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:04:09.137][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:09.138][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:09.139][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:04:09.140][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:09.142][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:04:09.143][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:04:09.144][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:09.145][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:09.151][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:04:09.152][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.251][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-10 19:04:09.257][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-10 19:04:09.259][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-10 19:04:09.261][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-10 19:04:09.263][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-10 19:04:09.265][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-10 19:04:09.267][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-10 19:04:09.269][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-10 19:04:09.270][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-10 19:04:09.272][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-10 19:04:09.275][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:04:09.277][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-10 19:04:09.278][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-10 19:04:09.281][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-10 19:04:09.290][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-10 19:04:09.292][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:04:09.294][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-10 19:04:09.296][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-10 19:04:09.298][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-10 19:04:09.300][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-10 19:04:09.302][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-10 19:04:09.303][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-10 19:04:09.305][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-10 19:04:09.307][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-10 19:04:09.309][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-10 19:04:09.311][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-10 19:04:09.312][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-10 19:04:09.314][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-10 19:04:09.316][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-10 19:04:09.317][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-10 19:04:09.319][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-10 19:04:09.321][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-10 19:04:09.322][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-10 19:04:09.324][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-10 19:04:09.326][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-10 19:04:09.328][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-10 19:04:09.330][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-10 19:04:09.331][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-10 19:04:09.333][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-10 19:04:09.335][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-10 19:04:09.337][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-10 19:04:09.339][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-10 19:04:09.341][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-10 19:04:09.343][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-10 19:04:09.344][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-10 19:04:09.346][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-10 19:04:09.348][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-10 19:04:09.350][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-10 19:04:09.352][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-10 19:04:09.354][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-10 19:04:09.355][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-10 19:04:09.357][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-10 19:04:09.359][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-10 19:04:09.361][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-10 19:04:09.363][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-10 19:04:09.365][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-10 19:04:09.366][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-10 19:04:09.368][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-10 19:04:09.370][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-10 19:04:09.372][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-10 19:04:09.374][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-10 19:04:09.375][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-10 19:04:09.376][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-10 19:04:09.378][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-10 19:04:09.379][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-10 19:04:09.381][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-10 19:04:09.383][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-10 19:04:09.384][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-10 19:04:09.386][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-10 19:04:09.387][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-10 19:04:09.389][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-10 19:04:09.391][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-10 19:04:09.392][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-10 19:04:09.394][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-10 19:04:09.396][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-10 19:04:09.398][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-10 19:04:09.400][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-10 19:04:09.401][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-10 19:04:09.403][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-10 19:04:09.404][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-10 19:04:09.406][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-10 19:04:09.408][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-10 19:04:09.409][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-10 19:04:09.418][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-10 19:04:09.420][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:04:09.425][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:04:09.425][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.427][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.428][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.DEBUG[2023-04-10 19:04:09.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:09.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:09.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:09.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:09.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:09.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:09.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:09.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:09.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:09.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:09.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:09.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:09.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.461][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[2023-04-10 19:04:09.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:09.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:09.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:09.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:09.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:09.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:09.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:09.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:09.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:09.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:09.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:09.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:09.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:09.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:09.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:09.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:09.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.504][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[2023-04-10 19:04:09.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:09.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:09.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:09.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:09.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:09.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:09.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:09.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:09.520][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-04-10 19:04:09.528][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-04-10 19:04:09.534][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:09.535][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-10 19:04:09.536][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.537][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:04:09.537][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.538][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:04:09.539][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.540][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:04:09.541][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:04:09.541][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:04:09.542][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.543][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-04-10 19:04:09.544][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:04:09.545][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-04-10 19:04:09.545][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-04-10 19:04:09.545][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-04-10 19:04:09.545][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-04-10 19:04:09.545][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-04-10 19:04:09.545][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-04-10 19:04:09.545][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-04-10 19:04:09.545][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-04-10 19:04:09.545][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-04-10 19:04:09.545][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:09.546][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:04:09.546][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:04:09.547][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:04:09.548][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:09.549][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:09.549][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:04:09.550][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:09.551][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:09.552][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:04:09.552][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-10 19:04:09.552][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-04-10 19:04:09.553][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:04:09.554][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:04:09.555][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:09.555][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:09.560][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-04-10 19:04:09.561][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:04:09.583][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-04-10 19:04:09.585][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-04-10 19:04:09.588][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-04-10 19:04:09.592][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-04-10 19:04:09.596][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-10 19:04:09.597][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-10 19:04:09.598][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-04-10 19:04:09.599][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-04-10 19:04:09.607][biodb::testThat]
biodb.INFO [2023-04-10 19:04:09.608][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-04-10 19:04:09.608][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:09.609][biodb::testThat]
biodb.TRACE[2023-04-10 19:04:09.614][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2023-04-10 19:04:09.616][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:04:09.621][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-10 19:04:09.630][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:09.631][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:09.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:09.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:09.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:09.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:09.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:09.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:09.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:09.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.682][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:04:09.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:04:09.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.686][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:04:09.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:04:09.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.690][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:09.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:09.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.726][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:09.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:09.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.731][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:09.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:09.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.735][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:09.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:09.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.739][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:04:09.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:09.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.742][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:04:09.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:09.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.745][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:09.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:09.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.749][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:09.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:09.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.752][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:09.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:09.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.756][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:09.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:09.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.759][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:04:09.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:09.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.762][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-10 19:04:09.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:09.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:09.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:09.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:09.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:09.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.773][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:04:09.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:09.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:09.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:09.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:09.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:09.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.846][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:09.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:09.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.849][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:09.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:09.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.853][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:09.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:09.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.856][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:09.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:09.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.859][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:09.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:09.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.866][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:09.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:09.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:04:09.892][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2023-04-10 19:04:09.894][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:04:09.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:04:09.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.898][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:04:09.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:04:09.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.902][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-10 19:04:09.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-10 19:04:09.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.905][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-10 19:04:09.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-10 19:04:09.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.937][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:09.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:09.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.972][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:09.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:09.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.975][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:09.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:09.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.978][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:09.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:09.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:09.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:09.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:09.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:09.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.000][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:10.001][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:10.002][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.002][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:10.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:10.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.013][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.018][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.022][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.026][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.027][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.028][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.029][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.031][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.041][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:10.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:10.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.045][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:10.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:10.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.048][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:10.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:10.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.051][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:10.052][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:10.053][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.054][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.055][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:10.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:10.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.064][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:10.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:10.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.067][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:10.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:10.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.071][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:10.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:10.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.074][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:10.075][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:10.076][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.076][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.077][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:10.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:10.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:10.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:10.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:10.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:10.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:10.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:10.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.102][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:10.103][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:10.104][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.105][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:10.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:10.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.116][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:10.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:10.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.119][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:10.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:10.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.122][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:10.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:10.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.126][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:10.127][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:10.127][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.128][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.129][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:10.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:10.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.138][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:10.139][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:10.139][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.140][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.144][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:10.145][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:10.146][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.147][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.151][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:10.152][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:10.153][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.153][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.157][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:10.163][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:10.164][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.165][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.170][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.171][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.171][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.172][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.177][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:10.178][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:10.179][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.179][ef$get] fields variable is a list.
biodb.INFO [2023-04-10 19:04:10.184][biodb::testThat]
biodb.INFO [2023-04-10 19:04:10.185][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-04-10 19:04:10.186][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:10.187][biodb::testThat]
biodb.DEBUG[2023-04-10 19:04:10.198][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2023-04-10 19:04:10.205][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:04:10.208][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2023-04-10 19:04:10.209][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:10.210][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2023-04-10 19:04:10.211][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:04:10.231][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:04:10.232][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-10 19:04:10.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:10.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:10.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:10.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:10.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:10.241][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:10.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:10.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:10.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:10.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:10.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:10.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.252][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:10.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:10.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:10.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:10.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.259][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:04:10.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:04:10.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.262][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:04:10.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:04:10.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.266][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:10.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:10.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.269][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:10.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:10.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.273][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:10.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:10.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.276][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:10.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:10.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.281][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:04:10.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:10.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.285][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:04:10.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:10.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.288][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:10.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:10.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.292][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:10.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:10.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.296][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.300][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.304][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:04:10.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.309][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-10 19:04:10.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.313][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.316][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.320][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:04:10.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.323][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.327][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.331][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.336][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.347][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.352][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:10.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:10.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.355][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:10.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:10.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:10.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:10.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.362][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:10.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:10.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:10.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:10.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:10.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:10.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:10.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:10.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:10.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:10.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:10.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:10.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:10.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:10.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:04:10.390][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2023-04-10 19:04:10.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-10 19:04:10.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-10 19:04:10.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-10 19:04:10.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-10 19:04:10.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.398][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-10 19:04:10.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-10 19:04:10.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:04:10.407][biodb::testThat]
biodb.INFO [2023-04-10 19:04:10.408][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-04-10 19:04:10.409][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:10.410][biodb::testThat]
biodb.TRACE[2023-04-10 19:04:10.412][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.413][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.414][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.415][ef$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:04:10.416][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2023-04-10 19:04:10.441][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:04:10.454][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-04-10 19:04:10.637][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[2023-04-10 19:04:10.653][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:10.668][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-04-10 19:04:10.670][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:10.672][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2023-04-10 19:04:10.674][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2023-04-10 19:04:10.690][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:10.692][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:10.693][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.694][ef$get] fields variable is a list.
biodb.INFO [2023-04-10 19:04:10.696][biodb::testThat]
biodb.INFO [2023-04-10 19:04:10.697][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-04-10 19:04:10.698][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:10.699][biodb::testThat]
biodb.TRACE[2023-04-10 19:04:10.718][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.722][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.725][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:10.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:10.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:04:10.843][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[2023-04-10 19:04:10.847][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:10.848][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-04-10 19:04:10.850][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:10.851][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2023-04-10 19:04:10.865][biodb::testThat]
biodb.INFO [2023-04-10 19:04:10.866][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-04-10 19:04:10.867][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:10.868][biodb::testThat]
biodb.TRACE[2023-04-10 19:04:10.883][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:04:10.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:04:10.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.887][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:04:10.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:04:10.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.896][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-10 19:04:10.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-10 19:04:10.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.901][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-10 19:04:10.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-10 19:04:10.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.948][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:04:10.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:04:10.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.952][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:04:10.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:04:10.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.955][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-10 19:04:10.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-10 19:04:10.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:10.959][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-10 19:04:10.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-10 19:04:10.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:10.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:04:10.967][biodb::testThat]
biodb.INFO [2023-04-10 19:04:10.968][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-04-10 19:04:10.969][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:10.970][biodb::testThat]
biodb.INFO [2023-04-10 19:04:10.976][biodb::testThat]
biodb.INFO [2023-04-10 19:04:10.977][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-04-10 19:04:10.978][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:10.980][biodb::testThat]
biodb.INFO [2023-04-10 19:04:10.985][biodb::testThat]
biodb.INFO [2023-04-10 19:04:10.986][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-04-10 19:04:10.987][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:10.987][biodb::testThat]
biodb.DEBUG[2023-04-10 19:04:10.991][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2023-04-10 19:04:12.584][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2023-04-10 19:04:13.334][biodb::testThat]
biodb.INFO [2023-04-10 19:04:13.336][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-04-10 19:04:13.337][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:13.338][biodb::testThat]
biodb.TRACE[2023-04-10 19:04:13.343][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:13.344][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:13.345][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:13.347][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:13.348][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:13.349][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:13.351][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:13.352][ef$get] fields variable is a list.
biodb.INFO [2023-04-10 19:04:13.354][biodb::testThat]
biodb.INFO [2023-04-10 19:04:13.355][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2023-04-10 19:04:13.356][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:13.357][biodb::testThat]
biodb.TRACE[2023-04-10 19:04:13.369][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:13.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:13.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:13.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:13.373][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:13.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:13.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:13.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:13.377][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:13.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:13.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:13.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:04:13.605][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[2023-04-10 19:04:13.608][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:13.609][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-04-10 19:04:13.610][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:13.612][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2023-04-10 19:04:13.724][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[2023-04-10 19:04:13.727][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:13.728][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-04-10 19:04:13.730][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:13.731][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2023-04-10 19:04:13.743][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:04:13.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:04:13.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:13.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:13.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:04:13.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:04:13.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:13.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:13.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:13.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:13.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:13.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:13.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:13.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:13.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:13.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:13.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:13.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:13.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:13.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:13.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:13.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:13.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:13.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:13.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:13.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:13.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:13.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:04:13.806][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[2023-04-10 19:04:13.810][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:13.812][cch$loadFileContent] Trying to load 1 files from cache: [1]: "304383a7dc8c451be84009e31d831359".
biodb.TRACE[2023-04-10 19:04:13.814][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:13.856][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content".
biodb.DEBUG[2023-04-10 19:04:15.066][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[2023-04-10 19:04:15.069][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:15.071][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7f71825f1888a7b29e4b8407502d21e3".
biodb.TRACE[2023-04-10 19:04:15.072][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:15.074][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content".
biodb.DEBUG[2023-04-10 19:04:15.115][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[2023-04-10 19:04:15.118][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:15.119][cch$loadFileContent] Trying to load 1 files from cache: [1]: "fd41c675dd237f33cdaafcbb15058c54".
biodb.TRACE[2023-04-10 19:04:15.121][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:15.122][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content".
biodb.TRACE[2023-04-10 19:04:15.141][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-10 19:04:15.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-10 19:04:15.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:15.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:04:15.153][biodb::testThat]
biodb.INFO [2023-04-10 19:04:15.154][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-04-10 19:04:15.156][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:15.157][biodb::testThat]
biodb.TRACE[2023-04-10 19:04:15.161][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:04:15.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:04:15.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:15.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:15.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:04:15.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:04:15.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:15.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:15.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:15.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:15.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:15.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:15.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:15.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:15.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:15.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:15.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:15.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:15.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:15.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:15.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:15.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:15.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:15.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:04:15.208][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:15.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:15.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:15.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:15.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:15.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:15.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:15.309][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[2023-04-10 19:04:15.312][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:15.314][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2023-04-10 19:04:15.315][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:15.369][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2023-04-10 19:04:16.363][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2023-04-10 19:04:16.412][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-04-10 19:04:16.414][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2023-04-10 19:04:16.416][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-04-10 19:04:16.419][loadFileContents] Loaded 2 files from 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[2023-04-10 19:04:16.421][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:04:16.422][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-04-10 19:04:16.424][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-10 19:04:16.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:16.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:16.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:16.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:16.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:16.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:16.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:16.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:16.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:16.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:16.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:16.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:16.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:16.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:16.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:16.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.460][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:04:16.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:04:16.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.464][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:04:16.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:04:16.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.469][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:16.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:16.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.473][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:16.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:16.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.478][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:16.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:16.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.481][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:16.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:16.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.485][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:04:16.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:16.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.489][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:04:16.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:16.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.510][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:16.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:16.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.514][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:16.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:16.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.518][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:16.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:16.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:16.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:16.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.525][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:04:16.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:16.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.529][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-10 19:04:16.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:16.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.532][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:16.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:16.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.535][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:16.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:16.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.539][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:04:16.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:16.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.542][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.546][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:16.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:16.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.554][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:16.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:16.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:16.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:16.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:16.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:16.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:04:16.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:16.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:16.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:16.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:16.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:16.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:16.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:16.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:16.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:16.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:16.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:16.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:16.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:16.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.597][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:04:16.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:04:16.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.601][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:04:16.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:04:16.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.604][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:16.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:16.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.608][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:16.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:16.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.612][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:16.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:16.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.615][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:16.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:16.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.620][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:04:16.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:16.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.625][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:04:16.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:16.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.630][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:16.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:16.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.635][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:16.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:16.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:16.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:16.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.659][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:16.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:16.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.663][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:04:16.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:16.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.667][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-10 19:04:16.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:16.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:16.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:16.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:16.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:16.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.680][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:04:16.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:16.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.683][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.687][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:16.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:16.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.694][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:16.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:16.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:16.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:16.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:16.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:16.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:16.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:16.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:16.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:16.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:16.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:16.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:16.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:16.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:16.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:16.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:16.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:16.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:04:16.729][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2023-04-10 19:04:16.737][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-10 19:04:16.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:16.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:16.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:16.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:16.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:16.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:16.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:16.748][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.752][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.756][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:16.757][private$selectFields]
biodb.TRACE[2023-04-10 19:04:16.758][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:04:16.759][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:04:16.760][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:16.761][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.761][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.762][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.763][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.764][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.765][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.766][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.766][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.767][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:16.768][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:16.769][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.770][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.772][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.772][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.773][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-10 19:04:16.774][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.791][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.794][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.805][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-04-10 19:04:16.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:16.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:16.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:16.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:16.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:16.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:16.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:16.820][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.825][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.829][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:16.830][private$selectFields]
biodb.TRACE[2023-04-10 19:04:16.831][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:04:16.832][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:04:16.833][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:16.834][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.835][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.836][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.837][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.838][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.840][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.841][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.842][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.843][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:16.844][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:16.845][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.846][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.847][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.848][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.849][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-10 19:04:16.850][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.854][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.857][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.861][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-04-10 19:04:16.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:16.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:16.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:16.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:16.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:16.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:16.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:16.871][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.876][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.881][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:16.882][private$selectFields]
biodb.TRACE[2023-04-10 19:04:16.883][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:04:16.884][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:04:16.885][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:16.886][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.888][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.889][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.890][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.891][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.893][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.894][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.895][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.896][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:16.897][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:16.898][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.899][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.900][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.901][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.902][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-10 19:04:16.903][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.908][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.913][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:16.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.919][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-04-10 19:04:16.920][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-10 19:04:16.921][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-10 19:04:16.944][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-10 19:04:16.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-10 19:04:16.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:04:16.949][biodb::testThat]
biodb.INFO [2023-04-10 19:04:16.950][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-04-10 19:04:16.951][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:16.951][biodb::testThat]
biodb.TRACE[2023-04-10 19:04:16.955][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:04:16.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:04:16.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:04:16.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:04:16.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:16.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:16.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:16.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:16.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:16.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:16.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:16.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:16.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:16.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:16.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:04:17.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:17.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:17.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:17.034][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:17.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:17.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:17.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:17.141][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[2023-04-10 19:04:17.145][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:17.146][cch$loadFileContent] Trying to load 1 files from cache: [1]: "5652f5994fce967a05a065a71bac3ed6".
biodb.TRACE[2023-04-10 19:04:17.148][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:17.181][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content".
biodb.DEBUG[2023-04-10 19:04:18.311][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-10 19:04:18.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:18.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:18.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:18.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:18.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:18.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:18.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:18.372][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.378][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.405][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:18.406][private$selectFields]
biodb.TRACE[2023-04-10 19:04:18.408][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:04:18.409][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:04:18.411][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:18.412][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.414][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.415][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.416][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.417][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.418][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.419][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.420][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.421][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:18.430][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:18.431][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.432][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.433][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.434][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.435][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-10 19:04:18.436][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.440][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.444][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.448][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-04-10 19:04:18.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:18.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:18.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:18.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:18.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:18.460][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:18.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:18.462][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.466][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.470][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:18.471][private$selectFields]
biodb.TRACE[2023-04-10 19:04:18.472][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:04:18.472][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:04:18.473][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:18.474][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.475][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.476][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.477][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.478][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.479][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.480][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.481][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.482][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:18.483][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:18.484][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.485][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.486][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.487][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.488][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-10 19:04:18.489][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.493][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.497][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.501][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-04-10 19:04:18.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:18.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:18.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:18.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:18.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:18.511][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:18.512][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.TRACE[2023-04-10 19:04:18.513][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.517][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.521][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:18.522][private$selectFields]
biodb.TRACE[2023-04-10 19:04:18.523][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:04:18.524][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:04:18.525][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:18.526][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.527][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.528][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.529][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.530][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.531][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.532][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.533][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.534][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:18.535][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:18.536][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.537][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.538][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.539][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.540][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-10 19:04:18.541][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.545][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.548][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:18.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.553][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-04-10 19:04:18.554][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-10 19:04:18.555][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-10 19:04:18.564][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-10 19:04:18.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-10 19:04:18.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:04:18.571][biodb::testThat]
biodb.INFO [2023-04-10 19:04:18.572][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-04-10 19:04:18.573][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:18.574][biodb::testThat]
biodb.TRACE[2023-04-10 19:04:18.577][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:04:18.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:04:18.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.582][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:04:18.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:04:18.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:18.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:18.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:18.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:18.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:18.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:18.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:18.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:18.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:18.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:18.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:04:18.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:18.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:18.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:18.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:18.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:18.621][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:18.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:18.726][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[2023-04-10 19:04:18.729][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:18.730][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2023-04-10 19:04:18.731][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:18.767][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2023-04-10 19:04:19.799][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-10 19:04:19.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:19.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:19.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:19.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:19.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:19.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:19.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:19.811][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.816][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.819][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:19.820][private$selectFields]
biodb.TRACE[2023-04-10 19:04:19.821][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:04:19.822][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:04:19.823][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:19.824][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.825][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.826][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.827][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.827][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.828][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.829][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.830][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.831][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:19.832][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:19.833][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.834][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.835][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.836][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.837][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-10 19:04:19.837][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.842][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.846][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.851][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-04-10 19:04:19.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:19.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:19.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:19.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:19.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:19.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:19.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:19.863][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.867][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.871][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:19.873][private$selectFields]
biodb.TRACE[2023-04-10 19:04:19.874][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:04:19.875][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:04:19.876][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:19.877][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.878][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.879][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.880][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.880][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.881][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.882][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.884][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.885][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:19.886][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:19.887][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.887][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.888][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.889][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.890][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-10 19:04:19.891][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.895][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.899][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.903][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-04-10 19:04:19.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:19.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:19.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:19.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:19.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:19.912][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:19.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:19.915][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.918][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.922][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:19.923][private$selectFields]
biodb.TRACE[2023-04-10 19:04:19.924][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:04:19.925][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:04:19.926][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:19.927][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.928][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.929][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.929][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.931][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.932][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.933][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.934][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.935][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:19.935][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:19.936][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.937][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.938][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.939][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.940][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-10 19:04:19.940][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.944][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.948][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:19.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:19.952][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-04-10 19:04:19.953][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-10 19:04:19.954][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-10 19:04:19.974][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-10 19:04:19.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-10 19:04:19.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:19.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:04:19.980][biodb::testThat]
biodb.INFO [2023-04-10 19:04:19.980][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2023-04-10 19:04:19.981][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:19.983][biodb::testThat]
biodb.DEBUG[2023-04-10 19:04:19.985][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-04-10 19:04:19.985][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:04:19.987][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-04-10 19:04:19.991][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:20.001][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv".
biodb.DEBUG[2023-04-10 19:04:20.002][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:04:20.003][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:04:20.004][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-10 19:04:20.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:20.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:20.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:20.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:20.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:20.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:20.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:20.016][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:20.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:20.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.019][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:20.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:20.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:04:20.050][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-04-10 19:04:20.051][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-04-10 19:04:20.057][biodb::testThat]
biodb.INFO [2023-04-10 19:04:20.058][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-04-10 19:04:20.059][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:20.060][biodb::testThat]
biodb.DEBUG[2023-04-10 19:04:20.079][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2023-04-10 19:04:20.081][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2023-04-10 19:04:20.082][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-04-10 19:04:20.084][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2023-04-10 19:04:20.091][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-04-10 19:04:20.100][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv".
biodb.DEBUG[2023-04-10 19:04:20.101][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:04:20.103][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-04-10 19:04:20.104][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-10 19:04:20.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:20.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:20.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:20.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:20.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:20.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:20.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:20.116][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:20.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:20.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.119][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:20.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:20.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:04:20.126][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:20.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:20.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:20.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:20.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:20.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:20.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:20.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:20.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:20.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:20.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:20.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.150][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:04:20.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:04:20.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.153][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:04:20.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:04:20.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.157][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:04:20.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:04:20.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.160][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:04:20.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:04:20.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.164][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:20.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:20.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.167][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:20.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:20.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.188][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:20.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:20.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.191][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:20.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:20.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.196][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:04:20.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:20.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.199][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:04:20.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:20.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.202][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:20.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:20.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.207][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:20.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:20.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.210][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:20.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:20.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.214][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:20.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:20.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.218][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:04:20.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:20.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.221][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-10 19:04:20.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:20.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.225][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:20.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:20.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.229][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:20.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:20.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.232][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:04:20.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:20.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.235][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:20.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:20.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.238][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:20.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:20.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.243][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:20.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:20.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:20.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:20.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.250][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:20.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:20.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.253][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:20.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:20.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.257][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:20.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:20.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.265][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:20.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:20.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:20.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:20.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:20.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:20.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:04:20.308][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2023-04-10 19:04:20.309][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-04-10 19:04:20.310][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-04-10 19:04:20.319][biodb::testThat]
biodb.INFO [2023-04-10 19:04:20.320][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2023-04-10 19:04:20.321][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:20.322][biodb::testThat]
biodb.INFO [2023-04-10 19:04:20.339][biodb::testThat]
biodb.INFO [2023-04-10 19:04:20.340][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2023-04-10 19:04:20.341][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:20.342][biodb::testThat]
biodb.INFO [2023-04-10 19:04:20.348][biodb::testThat]
biodb.INFO [2023-04-10 19:04:20.348][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2023-04-10 19:04:20.349][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:20.350][biodb::testThat]
biodb.DEBUG[2023-04-10 19:04:20.427][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[2023-04-10 19:04:20.432][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:20.433][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2023-04-10 19:04:20.435][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:20.465][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.TRACE[2023-04-10 19:04:21.516][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:21.518][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:21.519][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:21.520][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:21.521][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:21.521][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:21.522][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:21.524][ef$get] fields variable is a list.
biodb.INFO [2023-04-10 19:04:21.525][biodb::testThat]
biodb.INFO [2023-04-10 19:04:21.526][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2023-04-10 19:04:21.527][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:21.527][biodb::testThat]
biodb.ERROR[2023-04-10 19:04:21.539][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-04-10 19:04:21.553][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-04-10 19:04:21.562][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-10 19:04:21.563][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-04-10 19:04:21.564][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-04-10 19:04:21.565][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-10 19:04:21.565][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:21.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:21.567][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.569][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-10 19:04:21.578][biodb::testContext]
biodb.INFO [2023-04-10 19:04:21.579][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:04:21.580][biodb::testContext] Test context - Web services tests
biodb.INFO [2023-04-10 19:04:21.581][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:04:21.582][biodb::testContext]
biodb.INFO [2023-04-10 19:04:21.583][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:04:21.585][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-04-10 19:04:21.589][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:04:21.590][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-10 19:04:21.591][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-10 19:04:21.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.594][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-10 19:04:21.595][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-10 19:04:21.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.598][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-10 19:04:21.599][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-10 19:04:21.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.602][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-10 19:04:21.603][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-10 19:04:21.603][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-10 19:04:21.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.606][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-10 19:04:21.607][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-10 19:04:21.608][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-10 19:04:21.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.611][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-10 19:04:21.612][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-10 19:04:21.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.615][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-10 19:04:21.615][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-10 19:04:21.616][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-10 19:04:21.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.619][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-10 19:04:21.620][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-10 19:04:21.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.623][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-10 19:04:21.624][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-10 19:04:21.625][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-10 19:04:21.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.628][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:04:21.628][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-10 19:04:21.629][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-10 19:04:21.630][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-10 19:04:21.631][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-10 19:04:21.632][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-10 19:04:21.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.635][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-10 19:04:21.636][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-10 19:04:21.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.640][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-10 19:04:21.641][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-10 19:04:21.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.644][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-10 19:04:21.645][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-10 19:04:21.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.649][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-10 19:04:21.649][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-10 19:04:21.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.652][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[2023-04-10 19:04:21.652][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-10 19:04:21.653][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-10 19:04:21.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.656][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:04:21.657][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-10 19:04:21.678][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-10 19:04:21.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.682][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-10 19:04:21.683][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-10 19:04:21.684][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-10 19:04:21.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.688][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-10 19:04:21.690][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:21.691][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-10 19:04:21.692][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:21.693][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:04:21.694][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:21.694][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:04:21.695][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:21.696][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:04:21.697][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:04:21.698][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:04:21.699][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:21.700][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-10 19:04:21.701][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:04:21.702][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:21.703][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:21.704][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:04:21.704][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:04:21.704][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:04:21.704][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:04:21.704][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:04:21.705][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:04:21.706][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:21.707][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:21.708][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:04:21.709][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:21.709][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:21.710][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:04:21.712][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:21.713][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:04:21.713][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:04:21.714][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:21.715][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:21.716][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-10 19:04:21.718][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:21.719][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:04:21.720][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:21.720][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:04:21.721][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:21.722][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:04:21.723][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:21.724][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:04:21.724][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:04:21.725][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:04:21.726][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:21.727][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-10 19:04:21.728][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:04:21.729][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:21.730][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:21.730][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:04:21.730][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:04:21.730][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:04:21.730][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:04:21.730][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:04:21.731][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:04:21.732][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:21.733][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:21.734][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:04:21.735][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:21.736][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:21.737][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:04:21.737][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:21.738][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:04:21.739][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:04:21.740][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:21.741][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:21.742][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-10 19:04:21.743][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:21.744][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-10 19:04:21.745][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:21.746][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:04:21.747][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:21.747][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:04:21.748][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:21.749][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:04:21.750][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:04:21.751][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:04:21.751][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:21.752][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-10 19:04:21.753][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:04:21.754][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:21.755][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:21.755][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:21.756][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:04:21.757][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:21.758][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:21.758][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:04:21.759][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:21.760][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:21.761][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:04:21.762][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:21.762][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:04:21.763][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:04:21.764][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:21.765][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:21.766][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-10 19:04:21.767][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:21.768][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:04:21.769][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:21.769][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:04:21.770][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:21.771][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:04:21.772][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:21.773][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:04:21.774][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:04:21.774][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:04:21.775][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:21.776][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-10 19:04:21.777][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:04:21.778][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:21.778][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:21.779][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:21.780][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:04:21.781][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:21.781][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:21.782][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:04:21.783][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:21.784][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:21.784][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:04:21.785][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:21.786][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:04:21.787][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:04:21.788][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:21.788][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:21.789][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:04:21.790][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.791][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[2023-04-10 19:04:21.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.795][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[2023-04-10 19:04:21.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.862][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[2023-04-10 19:04:21.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.873][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-10 19:04:21.874][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-10 19:04:21.875][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-10 19:04:21.876][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-10 19:04:21.877][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-10 19:04:21.878][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-10 19:04:21.880][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-10 19:04:21.881][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-10 19:04:21.882][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-10 19:04:21.883][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-10 19:04:21.884][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:04:21.885][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-10 19:04:21.886][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-10 19:04:21.887][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-10 19:04:21.888][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-10 19:04:21.889][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:04:21.890][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-10 19:04:21.891][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-10 19:04:21.892][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-10 19:04:21.893][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-10 19:04:21.894][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-10 19:04:21.895][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-10 19:04:21.897][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-10 19:04:21.898][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-10 19:04:21.899][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-10 19:04:21.900][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-10 19:04:21.901][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-10 19:04:21.902][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-10 19:04:21.903][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-10 19:04:21.904][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-10 19:04:21.905][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-10 19:04:21.906][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-10 19:04:21.907][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-10 19:04:21.908][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-10 19:04:21.909][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-10 19:04:21.910][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-10 19:04:21.911][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-10 19:04:21.913][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-10 19:04:21.914][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-10 19:04:21.915][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-10 19:04:21.916][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-10 19:04:21.917][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-10 19:04:21.918][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-10 19:04:21.919][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-10 19:04:21.920][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-10 19:04:21.921][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-10 19:04:21.922][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-10 19:04:21.923][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-10 19:04:21.924][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-10 19:04:21.925][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-10 19:04:21.926][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-10 19:04:21.927][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-10 19:04:21.928][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-10 19:04:21.929][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-10 19:04:21.930][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-10 19:04:21.932][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-10 19:04:21.933][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-10 19:04:21.934][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-10 19:04:21.935][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-10 19:04:21.936][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-10 19:04:21.937][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-10 19:04:21.938][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-10 19:04:21.939][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-10 19:04:21.940][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-10 19:04:21.941][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-10 19:04:21.942][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-10 19:04:21.944][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-10 19:04:21.945][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-10 19:04:21.946][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-10 19:04:21.947][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-10 19:04:21.948][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-10 19:04:21.950][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-10 19:04:21.951][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-10 19:04:21.952][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-10 19:04:21.954][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-10 19:04:21.955][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-10 19:04:21.956][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-10 19:04:21.957][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-10 19:04:21.958][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-10 19:04:21.960][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-10 19:04:21.961][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-10 19:04:21.962][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-10 19:04:21.963][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-10 19:04:21.964][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-10 19:04:21.966][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:04:21.967][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:04:21.967][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.969][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:21.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:21.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:21.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:21.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:21.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:21.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:21.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:21.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:21.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:21.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:21.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:21.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:21.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:21.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:21.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:21.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:22.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:22.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:22.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:22.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:22.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:22.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:22.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:22.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:22.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:22.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:22.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:22.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:22.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:22.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:22.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:22.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:22.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:22.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:22.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:22.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:22.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:22.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:22.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:22.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:22.020][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[2023-04-10 19:04:22.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:22.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:22.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:22.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:22.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:22.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:22.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:22.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:22.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:22.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:22.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:22.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:22.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:22.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:22.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:22.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:22.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:22.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:22.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:22.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:22.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:22.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:22.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:22.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:22.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:22.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:22.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:22.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:22.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:22.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:22.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:22.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:22.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:22.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:22.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:22.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:22.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:22.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:22.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:22.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:22.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:22.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:22.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:22.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:22.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:22.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:22.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:22.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:22.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:22.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:22.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:22.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:22.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:22.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:22.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:22.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:22.066][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-04-10 19:04:22.067][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-04-10 19:04:22.069][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:22.070][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-10 19:04:22.071][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:22.072][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:04:22.073][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:22.073][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:04:22.074][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:22.075][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:04:22.076][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:04:22.077][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:04:22.078][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:22.079][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-04-10 19:04:22.080][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:04:22.081][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-04-10 19:04:22.081][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-04-10 19:04:22.081][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-04-10 19:04:22.081][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-04-10 19:04:22.081][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-04-10 19:04:22.081][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-04-10 19:04:22.081][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-04-10 19:04:22.081][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-04-10 19:04:22.081][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-04-10 19:04:22.082][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:22.083][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:04:22.083][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:04:22.084][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:04:22.085][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:22.086][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:22.087][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:04:22.087][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:22.088][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:22.089][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:04:22.090][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-10 19:04:22.090][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-04-10 19:04:22.091][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:04:22.091][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:04:22.092][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:22.093][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:22.094][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-04-10 19:04:22.095][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:04:22.098][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-04-10 19:04:22.099][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-04-10 19:04:22.100][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-04-10 19:04:22.101][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-04-10 19:04:22.102][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-10 19:04:22.103][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-10 19:04:22.105][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-04-10 19:04:22.105][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-04-10 19:04:22.107][biodb::testThat]
biodb.INFO [2023-04-10 19:04:22.108][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2023-04-10 19:04:22.108][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:22.109][biodb::testThat]
biodb.DEBUG[2023-04-10 19:04:22.202][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[2023-04-10 19:04:22.206][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:22.207][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cfd52aa1c2e3525a5defd7b7e8bd8bb8".
biodb.TRACE[2023-04-10 19:04:22.209][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:22.212][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content".
biodb.DEBUG[2023-04-10 19:04:22.286][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[2023-04-10 19:04:22.289][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:22.290][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4ae22a112f570b93d2a956448ab71bd0".
biodb.TRACE[2023-04-10 19:04:22.291][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:22.298][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content".
biodb.INFO [2023-04-10 19:04:22.305][biodb::testThat]
biodb.INFO [2023-04-10 19:04:22.307][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2023-04-10 19:04:22.308][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:22.308][biodb::testThat]
biodb.INFO [2023-04-10 19:04:22.334][biodb::testThat]
biodb.INFO [2023-04-10 19:04:22.335][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2023-04-10 19:04:22.336][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:22.337][biodb::testThat]
biodb.DEBUG[2023-04-10 19:04:22.418][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[2023-04-10 19:04:22.421][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:22.422][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2023-04-10 19:04:22.423][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:22.427][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2023-04-10 19:04:22.515][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[2023-04-10 19:04:22.518][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:22.519][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2023-04-10 19:04:22.520][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:22.522][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2023-04-10 19:04:22.592][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[2023-04-10 19:04:22.595][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:22.597][cch$loadFileContent] Trying to load 1 files from cache: [1]: "9edcc233717c530cf0cbf5f73b9c3fc7".
biodb.TRACE[2023-04-10 19:04:22.599][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:22.601][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content".
biodb.DEBUG[2023-04-10 19:04:22.685][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[2023-04-10 19:04:22.688][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:22.690][cch$loadFileContent] Trying to load 1 files from cache: [1]: "be9130a77f849b73da505cd10830451e".
biodb.TRACE[2023-04-10 19:04:22.691][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:22.703][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content".
biodb.DEBUG[2023-04-10 19:04:22.910][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[2023-04-10 19:04:22.914][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:22.915][cch$loadFileContent] Trying to load 1 files from cache: [1]: "6821b039f49696a2484834eb67daa971".
biodb.TRACE[2023-04-10 19:04:22.917][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:22.924][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content".
biodb.INFO [2023-04-10 19:04:23.054][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-10 19:04:23.055][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-04-10 19:04:23.056][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-04-10 19:04:23.057][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-10 19:04:23.058][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:23.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:23.059][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.061][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-10 19:04:23.065][biodb::testContext]
biodb.INFO [2023-04-10 19:04:23.065][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:04:23.066][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2023-04-10 19:04:23.067][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:04:23.068][biodb::testContext]
biodb.INFO [2023-04-10 19:04:23.069][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:04:23.071][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-04-10 19:04:23.091][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:04:23.092][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-10 19:04:23.093][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-10 19:04:23.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.097][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-10 19:04:23.098][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-10 19:04:23.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.100][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.DEBUG[2023-04-10 19:04:23.101][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-10 19:04:23.102][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-10 19:04:23.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.104][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-10 19:04:23.105][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-10 19:04:23.106][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-10 19:04:23.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.109][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-10 19:04:23.110][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-10 19:04:23.111][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-10 19:04:23.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.114][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-10 19:04:23.115][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-10 19:04:23.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.118][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-10 19:04:23.119][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-10 19:04:23.120][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-10 19:04:23.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.123][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-10 19:04:23.124][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-10 19:04:23.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.127][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-10 19:04:23.127][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-10 19:04:23.128][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-10 19:04:23.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.131][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:04:23.132][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-10 19:04:23.133][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-10 19:04:23.134][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-10 19:04:23.134][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-10 19:04:23.135][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-10 19:04:23.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.140][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-10 19:04:23.140][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-10 19:04:23.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.143][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-10 19:04:23.144][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-10 19:04:23.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.148][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-10 19:04:23.149][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-10 19:04:23.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.152][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-10 19:04:23.153][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-10 19:04:23.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.156][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-10 19:04:23.157][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-10 19:04:23.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.160][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:04:23.161][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-10 19:04:23.185][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-10 19:04:23.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.189][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-10 19:04:23.190][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-10 19:04:23.191][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-10 19:04:23.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.194][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-10 19:04:23.196][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:23.197][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-10 19:04:23.198][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.199][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:04:23.200][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.201][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:04:23.201][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:23.202][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:04:23.203][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:04:23.204][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:04:23.205][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.206][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-10 19:04:23.207][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:04:23.208][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:23.209][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.210][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:04:23.210][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:04:23.210][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:04:23.210][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:04:23.210][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:04:23.211][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:04:23.212][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:23.212][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:23.214][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:04:23.214][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:23.215][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:23.216][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:04:23.217][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:23.218][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:04:23.247][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:04:23.248][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:23.249][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:23.250][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-10 19:04:23.252][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:23.252][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:04:23.253][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.254][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:04:23.255][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.256][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:04:23.257][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:23.258][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:04:23.258][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:04:23.259][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:04:23.260][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.261][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-10 19:04:23.262][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:04:23.263][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:23.264][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.265][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:04:23.265][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:04:23.265][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:04:23.265][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:04:23.265][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:04:23.266][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:04:23.267][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:23.267][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:23.268][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:04:23.269][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:23.270][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:23.271][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:04:23.272][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:23.273][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:04:23.274][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:04:23.275][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:23.276][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:23.277][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-10 19:04:23.279][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.280][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-10 19:04:23.281][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.282][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:04:23.283][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.284][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:04:23.286][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:23.287][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:04:23.288][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:04:23.289][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:04:23.290][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:23.291][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-10 19:04:23.292][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:04:23.293][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:23.293][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.295][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:23.295][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:04:23.296][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:23.297][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:23.298][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:04:23.299][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:23.299][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:23.300][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:04:23.301][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:23.302][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:04:23.303][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:04:23.303][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:23.304][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:23.305][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-10 19:04:23.306][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.307][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:04:23.308][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.309][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:04:23.310][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.311][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:04:23.312][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:23.313][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:04:23.314][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:04:23.315][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:04:23.316][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:23.316][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-10 19:04:23.317][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:04:23.318][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:23.319][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.320][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:23.320][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:04:23.321][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:23.322][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:23.323][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:04:23.324][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:23.325][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:23.326][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:04:23.326][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:23.327][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:04:23.328][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:04:23.329][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:23.331][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:23.332][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:04:23.332][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.351][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[2023-04-10 19:04:23.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.377][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[2023-04-10 19:04:23.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.382][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[2023-04-10 19:04:23.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.404][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[2023-04-10 19:04:23.404][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-10 19:04:23.406][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-10 19:04:23.407][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-10 19:04:23.408][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-10 19:04:23.409][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-10 19:04:23.410][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-10 19:04:23.412][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-10 19:04:23.413][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-10 19:04:23.414][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-10 19:04:23.415][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-10 19:04:23.416][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:04:23.418][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-10 19:04:23.419][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-10 19:04:23.420][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-10 19:04:23.421][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-10 19:04:23.422][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:04:23.424][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-10 19:04:23.425][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-10 19:04:23.426][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-10 19:04:23.427][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-10 19:04:23.428][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-10 19:04:23.430][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-10 19:04:23.431][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-10 19:04:23.432][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-10 19:04:23.433][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-10 19:04:23.434][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-10 19:04:23.436][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-10 19:04:23.437][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-10 19:04:23.438][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-10 19:04:23.439][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-10 19:04:23.440][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-10 19:04:23.442][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-10 19:04:23.443][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-10 19:04:23.444][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-10 19:04:23.461][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-10 19:04:23.463][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-10 19:04:23.465][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-10 19:04:23.466][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-10 19:04:23.467][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-10 19:04:23.468][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-10 19:04:23.470][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-10 19:04:23.471][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-10 19:04:23.473][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-10 19:04:23.474][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-10 19:04:23.476][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-10 19:04:23.477][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-10 19:04:23.478][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-10 19:04:23.479][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-10 19:04:23.480][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-10 19:04:23.482][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-10 19:04:23.483][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-10 19:04:23.484][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-10 19:04:23.485][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-10 19:04:23.486][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-10 19:04:23.487][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-10 19:04:23.488][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-10 19:04:23.489][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-10 19:04:23.491][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-10 19:04:23.492][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-10 19:04:23.493][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-10 19:04:23.494][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-10 19:04:23.495][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-10 19:04:23.496][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-10 19:04:23.497][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-10 19:04:23.498][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-10 19:04:23.499][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-10 19:04:23.501][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-10 19:04:23.502][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-10 19:04:23.503][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-10 19:04:23.504][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-10 19:04:23.505][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-10 19:04:23.506][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-10 19:04:23.507][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-10 19:04:23.508][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-10 19:04:23.509][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-10 19:04:23.511][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-10 19:04:23.512][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-10 19:04:23.513][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-10 19:04:23.514][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-10 19:04:23.515][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-10 19:04:23.516][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-10 19:04:23.518][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-10 19:04:23.519][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-10 19:04:23.520][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-10 19:04:23.521][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:04:23.522][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:04:23.523][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.524][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:23.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:23.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:23.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:23.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:23.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:23.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:23.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:23.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:23.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:23.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:23.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:23.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:23.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:23.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:23.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:23.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:23.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:23.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:23.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:23.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:23.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:23.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.598][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[2023-04-10 19:04:23.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:23.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:23.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:23.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:23.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:23.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:23.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.687][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[2023-04-10 19:04:23.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:23.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:23.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:23.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:23.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:04:23.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:04:23.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:23.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:23.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:23.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:23.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:23.761][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[2023-04-10 19:04:23.762][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-04-10 19:04:23.782][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-04-10 19:04:23.790][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:23.791][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-10 19:04:23.792][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.793][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:04:23.794][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.795][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:04:23.815][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.817][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:04:23.819][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:04:23.820][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:04:23.840][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.843][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-04-10 19:04:23.844][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:04:23.846][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-04-10 19:04:23.846][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-04-10 19:04:23.846][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-04-10 19:04:23.846][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-04-10 19:04:23.846][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-04-10 19:04:23.846][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-04-10 19:04:23.846][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-04-10 19:04:23.846][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-04-10 19:04:23.846][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-04-10 19:04:23.847][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-10 19:04:23.865][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:04:23.865][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:04:23.867][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:04:23.868][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:23.869][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:23.869][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:04:23.870][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:04:23.871][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:04:23.872][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:04:23.873][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-10 19:04:23.873][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-04-10 19:04:23.874][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:04:23.875][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:04:23.876][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-10 19:04:23.877][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:04:23.879][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-04-10 19:04:23.881][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:04:23.885][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-04-10 19:04:23.886][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-04-10 19:04:23.887][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-04-10 19:04:23.889][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-04-10 19:04:23.891][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-10 19:04:23.892][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-10 19:04:23.894][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-04-10 19:04:23.895][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-04-10 19:04:23.896][biodb::testThat]
biodb.INFO [2023-04-10 19:04:23.897][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2023-04-10 19:04:23.897][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:04:23.898][biodb::testThat]
biodb.DEBUG[2023-04-10 19:04:23.982][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[2023-04-10 19:04:23.986][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:04:23.988][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2023-04-10 19:04:23.990][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:04:24.021][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2023-04-10 19:04:24.992][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2023-04-10 19:04:24.994][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-04-10 19:04:24.996][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2023-04-10 19:04:24.997][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-04-10 19:04:24.998][loadFileContents] Loaded 2 files from 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[2023-04-10 19:04:24.999][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:04:25.001][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-04-10 19:04:25.002][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-10 19:04:25.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:25.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:25.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:25.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:25.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:25.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:25.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:25.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.034][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:04:25.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:04:25.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.038][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:04:25.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:04:25.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.042][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.046][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.050][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.055][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.060][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:04:25.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.064][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:04:25.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.068][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:25.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:25.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.071][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:25.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:25.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.075][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.078][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.081][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:04:25.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.085][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-10 19:04:25.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.089][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.093][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.096][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:04:25.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.100][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.103][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.107][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.111][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.115][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.119][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.123][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.132][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:04:25.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:25.151][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:25.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:25.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:25.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:25.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:25.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:25.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.180][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:04:25.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:04:25.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.183][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:04:25.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:04:25.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.186][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.190][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.193][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.196][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.200][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:04:25.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.203][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:04:25.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.206][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:25.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:25.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.209][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:25.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:25.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.213][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.217][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.220][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:04:25.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.224][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-10 19:04:25.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.228][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.231][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.234][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:04:25.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.237][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.241][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.247][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:04:25.282][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2023-04-10 19:04:25.285][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-10 19:04:25.286][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:25.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:25.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:25.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:25.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:25.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:25.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:25.298][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:04:25.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:04:25.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.302][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:04:25.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:04:25.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.305][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-10 19:04:25.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-10 19:04:25.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.309][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-10 19:04:25.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-10 19:04:25.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.312][private$selectFields] Fields none
biodb.TRACE[2023-04-10 19:04:25.313][private$selectFields]
biodb.TRACE[2023-04-10 19:04:25.314][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-04-10 19:04:25.333][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:04:25.334][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:25.336][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.337][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.338][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.339][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.339][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.340][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.341][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.342][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.343][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.343][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.345][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.345][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.346][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.347][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.348][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.349][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.349][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.350][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.351][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.352][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.353][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:25.353][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:25.354][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.355][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.356][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.356][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.357][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.358][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.359][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.360][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.360][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.361][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.362][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.363][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.363][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.364][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.365][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.366][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.367][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.368][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.369][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.370][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.371][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.372][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.373][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.374][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.374][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.375][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.376][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.377][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.378][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.379][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.380][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:25.381][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:25.381][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.382][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.383][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.384][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.385][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.386][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.387][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.388][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.389][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.390][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.391][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:25.392][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:25.393][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.394][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.395][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.396][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.397][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.397][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.398][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.399][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.400][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.401][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.402][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.402][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.403][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.404][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.405][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.406][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.407][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.408][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.409][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.409][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.410][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:25.411][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:25.412][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.413][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.414][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.415][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.416][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.416][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.417][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.418][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.419][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.420][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.420][private$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[2023-04-10 19:04:25.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.443][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.447][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.450][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.454][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.457][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.461][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.476][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:25.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:25.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.480][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:25.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:25.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.483][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:25.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:25.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.487][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.495][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.499][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.502][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.506][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.515][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2023-04-10 19:04:25.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:04:25.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:25.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:25.523][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:25.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:25.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:25.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:04:25.529][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:04:25.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:04:25.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.533][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:04:25.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:04:25.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.538][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-10 19:04:25.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-10 19:04:25.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.542][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-10 19:04:25.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-10 19:04:25.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.546][private$selectFields] Fields none
biodb.TRACE[2023-04-10 19:04:25.547][private$selectFields]
biodb.TRACE[2023-04-10 19:04:25.548][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-04-10 19:04:25.549][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:04:25.550][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:25.551][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.552][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.553][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.554][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.555][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.556][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.557][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.558][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.560][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.561][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.562][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.562][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.563][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.565][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.565][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.566][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.567][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.568][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.569][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.570][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.570][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:25.571][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:25.572][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.573][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.574][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.575][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.576][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.576][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.577][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.578][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.579][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.580][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.581][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.582][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.582][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.583][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.584][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.585][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.586][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.587][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.588][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.589][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.589][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.590][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.591][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.592][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.593][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.594][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.595][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.596][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.597][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.598][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.599][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:25.600][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:25.600][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.601][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.602][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.603][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.604][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.605][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.605][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.606][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.607][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.608][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.609][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:25.610][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:04:25.611][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.612][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.613][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.614][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.614][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.615][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.616][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.617][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.618][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.619][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.620][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.620][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.621][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.622][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.623][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.624][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.625][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.626][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.626][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.627][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.628][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:25.629][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:25.630][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.631][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.632][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.632][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.633][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.634][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.635][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.636][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.637][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.638][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.638][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2023-04-10 19:04:25.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:04:25.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:04:25.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:04:25.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.676][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.679][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.683][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:04:25.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.687][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.690][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.693][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:04:25.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:04:25.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.708][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:25.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:25.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.711][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:25.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:25.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.714][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:04:25.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:04:25.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.718][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.721][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.724][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:04:25.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:04:25.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.728][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.732][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.735][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:04:25.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:04:25.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:04:25.742][private$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[2023-04-10 19:04:25.742][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-04-10 19:04:25.743][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2023-04-10 19:04:25.746][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-10 19:04:25.746][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-04-10 19:04:25.748][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-04-10 19:04:25.748][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-10 19:04:25.749][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:04:25.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:04:25.750][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:04:25.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:04:25.752][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:04:25.754][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".
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 163 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 163 ]
> 
> proc.time()
   user  system elapsed 
 15.655   0.853  19.136

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn2.1050.7842.970
LipidmapsStructureEntry0.3450.0150.371