Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:37 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 merida1


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 181/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.2.0  (landing page)
Pierrick Roger
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_15
git_last_commit: 484c60e
git_last_commit_date: 2022-04-26 12:19:54 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: biodbLipidmaps
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.2.0.tar.gz
StartedAt: 2022-10-18 23:48:43 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 23:52:31 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 228.3 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbLipidmaps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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 [2022-10-18 23:50:02.176][biodb::testContext]
biodb.INFO [2022-10-18 23:50:02.192][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 23:50:02.194][biodb::testContext] Test context - Generic tests
biodb.INFO [2022-10-18 23:50:02.196][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 23:50:02.198][biodb::testContext]
biodb.INFO [2022-10-18 23:50:02.229][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 23:50:02.231][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 23:50:02.243][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:50:02.245][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 23:50:02.247][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 23:50:02.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.255][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 23:50:02.290][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 23:50:02.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.296][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 23:50:02.299][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 23:50:02.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.305][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 23:50:02.306][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 23:50:02.307][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 23:50:02.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.315][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 23:50:02.317][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 23:50:02.319][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 23:50:02.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.325][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 23:50:02.327][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 23:50:02.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.334][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 23:50:02.336][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 23:50:02.338][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 23:50:02.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.346][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 23:50:02.348][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 23:50:02.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.356][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 23:50:02.358][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 23:50:02.360][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 23:50:02.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.366][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 23:50:02.368][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 23:50:02.370][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 23:50:02.372][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 23:50:02.375][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 23:50:02.377][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 23:50:02.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.385][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 23:50:02.387][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 23:50:02.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.394][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 23:50:02.396][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 23:50:02.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.403][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 23:50:02.405][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 23:50:02.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.411][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 23:50:02.413][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 23:50:02.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.420][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 23:50:02.422][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 23:50:02.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.429][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 23:50:02.431][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 23:50:02.441][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-10-18 23:50:02.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.446][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[2022-10-18 23:50:02.448][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 23:50:02.449][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 23:50:02.451][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 23:50:02.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.463][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 23:50:02.544][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:02.575][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-18 23:50:02.577][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:02.579][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:50:02.581][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:02.583][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:50:02.585][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:02.587][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:50:02.589][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 23:50:02.591][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:50:02.593][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:02.595][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 23:50:02.597][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:50:02.599][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:02.601][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:02.603][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:50:02.603][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:50:02.603][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 23:50:02.603][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 23:50:02.603][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 23:50:02.605][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:50:02.607][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:02.608][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:02.610][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:50:02.613][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:02.614][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:02.616][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:50:02.618][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:02.620][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:50:02.621][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:50:02.623][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:02.626][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:02.628][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 23:50:02.631][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:02.633][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 23:50:02.635][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:02.637][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:50:02.638][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:02.639][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:50:02.642][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:02.644][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:50:02.646][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 23:50:02.648][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:50:02.650][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:02.653][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 23:50:02.655][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:50:02.657][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:02.659][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:02.661][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:50:02.661][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:50:02.661][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 23:50:02.661][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 23:50:02.661][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 23:50:02.663][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:50:02.664][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:02.666][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:02.668][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:50:02.670][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:02.672][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:02.674][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:50:02.676][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:02.678][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:50:02.679][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:50:02.680][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:02.682][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:02.684][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 23:50:02.688][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:02.691][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-18 23:50:02.693][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:02.695][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:50:02.697][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:02.699][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:50:02.702][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:02.704][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:50:02.706][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 23:50:02.708][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:50:02.710][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:02.711][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 23:50:02.712][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:50:02.714][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:02.715][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:02.717][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:02.719][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:50:02.721][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:02.723][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:02.725][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:50:02.726][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:02.727][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:02.729][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:50:02.731][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:02.733][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:50:02.734][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:50:02.736][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:02.739][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:02.741][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 23:50:02.744][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:02.745][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 23:50:02.746][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:02.748][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:50:02.749][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:02.751][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:50:02.753][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:02.754][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:50:02.756][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 23:50:02.758][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:50:02.760][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:02.762][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 23:50:02.764][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:50:02.766][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:02.768][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:02.770][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:02.772][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:50:02.774][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:02.775][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:02.777][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:50:02.779][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:02.781][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:02.782][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:50:02.784][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:02.785][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:50:02.786][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:50:02.788][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:02.790][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:02.796][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:50:02.798][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.799][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[2022-10-18 23:50:02.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.862][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[2022-10-18 23:50:02.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.870][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[2022-10-18 23:50:02.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:02.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.952][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 23:50:02.962][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 23:50:02.965][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 23:50:02.968][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 23:50:02.971][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 23:50:02.974][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 23:50:02.977][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 23:50:02.980][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 23:50:02.983][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 23:50:02.985][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 23:50:02.987][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 23:50:02.990][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 23:50:02.993][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 23:50:02.996][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 23:50:02.998][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 23:50:03.001][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 23:50:03.003][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 23:50:03.006][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 23:50:03.009][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 23:50:03.011][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 23:50:03.014][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 23:50:03.017][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 23:50:03.020][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 23:50:03.024][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 23:50:03.027][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 23:50:03.030][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 23:50:03.033][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 23:50:03.036][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 23:50:03.039][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 23:50:03.041][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 23:50:03.043][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 23:50:03.046][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 23:50:03.049][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 23:50:03.053][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 23:50:03.056][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 23:50:03.059][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 23:50:03.061][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 23:50:03.064][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 23:50:03.067][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 23:50:03.070][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 23:50:03.072][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 23:50:03.075][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 23:50:03.078][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 23:50:03.082][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 23:50:03.084][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 23:50:03.087][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 23:50:03.090][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 23:50:03.093][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 23:50:03.096][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 23:50:03.099][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 23:50:03.102][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 23:50:03.106][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 23:50:03.109][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 23:50:03.119][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 23:50:03.121][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 23:50:03.125][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 23:50:03.128][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 23:50:03.131][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 23:50:03.133][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 23:50:03.136][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 23:50:03.139][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 23:50:03.141][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 23:50:03.144][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 23:50:03.146][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 23:50:03.149][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 23:50:03.152][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 23:50:03.155][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 23:50:03.158][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 23:50:03.160][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 23:50:03.161][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 23:50:03.164][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 23:50:03.167][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 23:50:03.170][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 23:50:03.173][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 23:50:03.176][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 23:50:03.178][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 23:50:03.180][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 23:50:03.182][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 23:50:03.185][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 23:50:03.188][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 23:50:03.190][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 23:50:03.193][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 23:50:03.196][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 23:50:03.209][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 23:50:03.213][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 23:50:03.219][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:50:03.221][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.225][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:03.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:03.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:03.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:03.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:03.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:03.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:03.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:03.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:03.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:03.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:03.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:03.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:03.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:03.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:03.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:03.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:03.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:03.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:03.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:03.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:03.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:03.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:03.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:03.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:03.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:03.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.393][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[2022-10-18 23:50:03.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:03.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:03.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:03.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.456][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[2022-10-18 23:50:03.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:03.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:03.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:03.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:03.480][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-10-18 23:50:03.498][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 23:50:03.502][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:03.505][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 23:50:03.507][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:03.509][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:50:03.511][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:03.513][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:50:03.516][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:03.518][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:50:03.520][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 23:50:03.522][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:50:03.525][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:03.527][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-10-18 23:50:03.529][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:50:03.531][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-10-18 23:50:03.531][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-10-18 23:50:03.531][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-10-18 23:50:03.531][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-10-18 23:50:03.531][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-10-18 23:50:03.531][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-10-18 23:50:03.531][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-10-18 23:50:03.531][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-10-18 23:50:03.531][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-10-18 23:50:03.534][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:03.536][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:50:03.536][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:50:03.538][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:50:03.540][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:03.542][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:03.544][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:50:03.546][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:03.548][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:03.550][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:50:03.552][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 23:50:03.552][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-10-18 23:50:03.554][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:50:03.556][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:50:03.558][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:03.560][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:03.573][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-10-18 23:50:03.576][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 23:50:03.624][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 23:50:03.626][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-10-18 23:50:03.635][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 23:50:03.644][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-10-18 23:50:03.653][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-10-18 23:50:03.655][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-10-18 23:50:03.658][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-10-18 23:50:03.661][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-10-18 23:50:03.695][biodb::testThat]
biodb.INFO [2022-10-18 23:50:03.697][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2022-10-18 23:50:03.699][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:03.702][biodb::testThat]
biodb.TRACE[2022-10-18 23:50:03.709][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[2022-10-18 23:50:03.721][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:03.730][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-10-18 23:50:03.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:03.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:03.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:03.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:03.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:03.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:03.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:03.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:03.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.875][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 23:50:03.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 23:50:03.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.882][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:03.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:03.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.890][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:03.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:03.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.952][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:03.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:03.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.965][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:03.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:03.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.974][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:03.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:03.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.987][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 23:50:03.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:03.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.995][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 23:50:03.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:04.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.010][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:04.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:04.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.018][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:04.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:04.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.032][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:04.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:04.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.041][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:04.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:04.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.062][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 23:50:04.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:04.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.071][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 23:50:04.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:04.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.079][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:04.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:04.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:04.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:04.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.096][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 23:50:04.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:04.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.147][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:04.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:04.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.154][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:04.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:04.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.235][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:04.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:04.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.244][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:04.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:04.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.252][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:04.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:04.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.266][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:04.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:04.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.274][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:04.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:04.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.297][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:04.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:04.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:04.350][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2022-10-18 23:50:04.360][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 23:50:04.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 23:50:04.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.367][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 23:50:04.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 23:50:04.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.373][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 23:50:04.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 23:50:04.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.381][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 23:50:04.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 23:50:04.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.453][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:04.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:04.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.523][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:04.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:04.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.530][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:04.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:04.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.535][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:04.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:04.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.576][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.578][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.579][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.580][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.602][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:04.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:04.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.608][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:04.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:04.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.616][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:04.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:04.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.622][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:04.623][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:04.624][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.625][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.627][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:04.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:04.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.648][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:04.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:04.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.655][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:04.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:04.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.663][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:04.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:04.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.672][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:04.674][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:04.676][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.678][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.680][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:04.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:04.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.702][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:04.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:04.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.710][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:04.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:04.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.718][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:04.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:04.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.726][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:04.728][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:04.730][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.733][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.735][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:04.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:04.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:04.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:04.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:04.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:04.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:04.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:04.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.785][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:04.786][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:04.788][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.790][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:04.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:04.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.814][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:04.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:04.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.823][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:04.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:04.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.831][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:04.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:04.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.839][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:04.841][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:04.843][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.845][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.847][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:04.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:04.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.868][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:04.870][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:04.871][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.873][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.883][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:04.885][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:04.887][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.890][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.901][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:04.903][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:04.905][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.907][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.916][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:04.918][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:04.920][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.922][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.930][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:04.932][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:04.933][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.934][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:04.944][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:04.947][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:04.949][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:04.951][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 23:50:04.962][biodb::testThat]
biodb.INFO [2022-10-18 23:50:04.963][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2022-10-18 23:50:04.965][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:04.973][biodb::testThat]
biodb.DEBUG[2022-10-18 23:50:05.000][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2022-10-18 23:50:05.016][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:05.021][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2022-10-18 23:50:05.023][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:05.026][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2022-10-18 23:50:05.028][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:05.120][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:05.121][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-10-18 23:50:05.124][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:05.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:05.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:05.138][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:05.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:05.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:05.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:05.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:05.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:05.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:05.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:05.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:05.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:05.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.181][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:05.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:05.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.195][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 23:50:05.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 23:50:05.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.212][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:05.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:05.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.218][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:05.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:05.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.226][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:05.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:05.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.240][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:05.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:05.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.248][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:05.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:05.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.262][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 23:50:05.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:05.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.270][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 23:50:05.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:05.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.284][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:05.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:05.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.292][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:05.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:05.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.306][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:05.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:05.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.313][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:05.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:05.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.327][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 23:50:05.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:05.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.336][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 23:50:05.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:05.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:05.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:05.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.350][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:05.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:05.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.359][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 23:50:05.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:05.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.374][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:05.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:05.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.381][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:05.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:05.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.390][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:05.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:05.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:05.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:05.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.406][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:05.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:05.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.420][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:05.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:05.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.429][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:05.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:05.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:05.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:05.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.454][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:05.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:05.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:05.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:05.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:05.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:05.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:05.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:05.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:05.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:05.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:05.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:05.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:05.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:05.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:05.518][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2022-10-18 23:50:05.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-10-18 23:50:05.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-10-18 23:50:05.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-10-18 23:50:05.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-10-18 23:50:05.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-10-18 23:50:05.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-10-18 23:50:05.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 23:50:05.558][biodb::testThat]
biodb.INFO [2022-10-18 23:50:05.560][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2022-10-18 23:50:05.563][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:05.565][biodb::testThat]
biodb.TRACE[2022-10-18 23:50:05.571][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:05.574][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:05.576][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.578][ef$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:05.580][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2022-10-18 23:50:05.633][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:05.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:05.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.639][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:05.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:05.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:05.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:05.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:05.660][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-10-18 23:50:05.964][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[2022-10-18 23:50:06.010][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:06.012][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:06.016][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2022-10-18 23:50:13.996][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2022-10-18 23:50:14.639][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:14.656][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2022-10-18 23:50:14.704][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2022-10-18 23:50:14.714][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2022-10-18 23:50:14.782][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:14.784][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:14.786][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.788][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 23:50:14.792][biodb::testThat]
biodb.INFO [2022-10-18 23:50:14.793][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2022-10-18 23:50:14.795][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:14.797][biodb::testThat]
biodb.TRACE[2022-10-18 23:50:14.856][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:14.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:14.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.861][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:14.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:14.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.869][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:14.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:14.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:15.291][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-10-18 23:50:15.299][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:15.335][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-10-18 23:50:15.337][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:15.341][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2022-10-18 23:50:15.369][biodb::testThat]
biodb.INFO [2022-10-18 23:50:15.371][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2022-10-18 23:50:15.373][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:15.376][biodb::testThat]
biodb.TRACE[2022-10-18 23:50:15.433][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 23:50:15.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 23:50:15.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.443][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 23:50:15.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 23:50:15.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.451][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 23:50:15.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 23:50:15.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.459][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 23:50:15.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 23:50:15.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.579][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 23:50:15.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 23:50:15.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.589][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 23:50:15.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 23:50:15.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.599][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 23:50:15.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 23:50:15.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.609][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 23:50:15.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 23:50:15.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 23:50:15.623][biodb::testThat]
biodb.INFO [2022-10-18 23:50:15.625][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2022-10-18 23:50:15.627][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:15.629][biodb::testThat]
biodb.INFO [2022-10-18 23:50:15.641][biodb::testThat]
biodb.INFO [2022-10-18 23:50:15.643][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2022-10-18 23:50:15.646][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:15.648][biodb::testThat]
biodb.INFO [2022-10-18 23:50:15.658][biodb::testThat]
biodb.INFO [2022-10-18 23:50:15.661][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2022-10-18 23:50:15.663][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:15.666][biodb::testThat]
biodb.DEBUG[2022-10-18 23:50:15.675][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2022-10-18 23:50:16.442][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2022-10-18 23:50:16.907][biodb::testThat]
biodb.INFO [2022-10-18 23:50:16.909][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2022-10-18 23:50:16.911][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:16.912][biodb::testThat]
biodb.TRACE[2022-10-18 23:50:16.946][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:16.948][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:16.950][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:16.952][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:16.954][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:16.956][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:16.958][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:16.959][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 23:50:16.961][biodb::testThat]
biodb.INFO [2022-10-18 23:50:16.963][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2022-10-18 23:50:16.965][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:16.967][biodb::testThat]
biodb.TRACE[2022-10-18 23:50:16.996][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:16.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:17.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.004][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:17.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:17.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.011][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:17.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:17.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:17.426][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-10-18 23:50:17.432][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:17.434][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-10-18 23:50:17.437][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:17.440][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2022-10-18 23:50:17.763][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-10-18 23:50:17.770][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:17.773][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-10-18 23:50:17.775][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:17.778][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2022-10-18 23:50:17.809][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 23:50:17.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 23:50:17.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:17.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:17.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:17.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:17.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:17.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:17.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:17.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:17.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:17.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:17.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:17.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:17.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:18.023][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2022-10-18 23:50:18.060][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:18.062][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:18.097][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2022-10-18 23:50:22.897][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2022-10-18 23:50:29.366][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:29.381][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2022-10-18 23:50:29.441][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2022-10-18 23:50:30.127][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[2022-10-18 23:50:30.134][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:30.136][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:30.141][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2022-10-18 23:50:30.823][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2022-10-18 23:50:31.550][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:31.564][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2022-10-18 23:50:31.595][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2022-10-18 23:50:31.750][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2022-10-18 23:50:31.755][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:31.758][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:31.762][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2022-10-18 23:50:32.488][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2022-10-18 23:50:33.171][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:33.186][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2022-10-18 23:50:33.256][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2022-10-18 23:50:33.297][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 23:50:33.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 23:50:33.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 23:50:33.323][biodb::testThat]
biodb.INFO [2022-10-18 23:50:33.325][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2022-10-18 23:50:33.327][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:33.329][biodb::testThat]
biodb.TRACE[2022-10-18 23:50:33.335][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 23:50:33.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 23:50:33.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:33.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:33.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:33.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:33.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:33.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:33.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:33.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:33.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:33.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:33.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:33.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:33.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:33.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:33.424][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:33.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:33.671][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[2022-10-18 23:50:33.678][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:33.680][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:33.685][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2022-10-18 23:50:38.590][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2022-10-18 23:50:45.089][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2022-10-18 23:50:45.099][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2022-10-18 23:50:45.108][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2022-10-18 23:50:45.242][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2022-10-18 23:50:45.789][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2022-10-18 23:50:45.897][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-10-18 23:50:45.900][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2022-10-18 23:50:45.903][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2022-10-18 23:50:45.905][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:45.907][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:45.910][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 23:50:45.912][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:45.914][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:45.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:45.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:45.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:45.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:45.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:45.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:45.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:45.967][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2022-10-18 23:50:45.972][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:45.974][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:45.976][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2022-10-18 23:50:46.616][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2022-10-18 23:50:47.330][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:47.345][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2022-10-18 23:50:47.369][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2022-10-18 23:50:47.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:47.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:47.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:47.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:47.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:47.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:47.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:47.399][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2022-10-18 23:50:47.405][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:47.407][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:47.410][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2022-10-18 23:50:48.067][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2022-10-18 23:50:48.754][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:48.770][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2022-10-18 23:50:48.796][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2022-10-18 23:50:48.820][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2022-10-18 23:50:48.830][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:48.911][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-10-18 23:50:48.914][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-10-18 23:50:48.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:48.919][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:48.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:48.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:48.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:48.933][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:48.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:48.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:48.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:48.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:48.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:48.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:48.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:48.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:48.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:48.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:48.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:48.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:48.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:48.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:48.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:48.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:48.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:48.989][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 23:50:48.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 23:50:48.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:48.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:48.998][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:49.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:49.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.007][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:49.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:49.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.015][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:49.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:49.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.030][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:49.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:49.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.038][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:49.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:49.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.053][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 23:50:49.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.061][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 23:50:49.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.076][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:49.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:49.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.085][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:49.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:49.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.100][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:49.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:49.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.109][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:49.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:49.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.123][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 23:50:49.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:49.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.131][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 23:50:49.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:49.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.140][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:49.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:49.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.149][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:49.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:49.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.157][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 23:50:49.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:49.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.172][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.180][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:49.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:49.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.195][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:49.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:49.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:49.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:49.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:49.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:49.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:49.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:49.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:49.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:49.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:49.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:49.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:49.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:49.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:49.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:49.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:49.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:49.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.296][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 23:50:49.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 23:50:49.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.305][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:49.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:49.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.314][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:49.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:49.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.323][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:49.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:50:49.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.336][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:49.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:49.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.343][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:49.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:50:49.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.357][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 23:50:49.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.366][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 23:50:49.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.380][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:49.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:49.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.389][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:49.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:49.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.404][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:49.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:49.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.412][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:49.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:49.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.427][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 23:50:49.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:49.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.434][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 23:50:49.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:49.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.442][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:49.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:49.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.451][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:49.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:49.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.459][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 23:50:49.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:49.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.474][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.482][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:49.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:49.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.499][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:49.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:49.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:49.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:49.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:49.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:49.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:49.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:49.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:49.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:49.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:49.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:49.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:49.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:49.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:49.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:49.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:49.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:49.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:49.609][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2022-10-18 23:50:49.630][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 23:50:49.633][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:49.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:49.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:49.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:49.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:49.653][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:49.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:49.657][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.665][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.674][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:50:49.676][private$selectFields]
biodb.TRACE[2022-10-18 23:50:49.678][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:50:49.680][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:50:49.682][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:50:49.685][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.687][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.689][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.691][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.693][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.695][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.697][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.699][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.701][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:50:49.704][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:50:49.706][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.708][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.710][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.712][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.714][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 23:50:49.716][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.725][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.733][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.762][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-10-18 23:50:49.764][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:49.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:49.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:49.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:49.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:49.781][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:49.783][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.TRACE[2022-10-18 23:50:49.785][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.794][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.802][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:50:49.804][private$selectFields]
biodb.TRACE[2022-10-18 23:50:49.806][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:50:49.808][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:50:49.810][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:50:49.812][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.814][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.816][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.818][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.821][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.823][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.825][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.827][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.829][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:50:49.831][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:50:49.832][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.835][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.836][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.838][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.840][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 23:50:49.843][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.851][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.859][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.868][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-10-18 23:50:49.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:49.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:49.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:49.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:49.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:49.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:49.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:49.893][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.903][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.911][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:50:49.914][private$selectFields]
biodb.TRACE[2022-10-18 23:50:49.916][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:50:49.918][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:50:49.920][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:50:49.922][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.925][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.927][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.929][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.931][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.934][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.936][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.937][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.940][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:50:49.942][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:50:49.944][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.946][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.948][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.950][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.952][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 23:50:49.954][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.963][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.972][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:50:49.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.981][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-10-18 23:50:49.983][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 23:50:49.985][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 23:50:50.003][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 23:50:50.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 23:50:50.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 23:50:50.013][biodb::testThat]
biodb.INFO [2022-10-18 23:50:50.016][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2022-10-18 23:50:50.018][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:50.020][biodb::testThat]
biodb.TRACE[2022-10-18 23:50:50.027][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 23:50:50.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 23:50:50.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:50.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:50.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:50.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:50.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:50.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:50.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:50.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:50.463][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:50.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:50.732][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2022-10-18 23:50:50.739][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:50.741][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:50.745][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2022-10-18 23:50:56.605][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2022-10-18 23:51:03.077][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2022-10-18 23:51:03.087][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2022-10-18 23:51:03.097][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2022-10-18 23:51:03.161][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2022-10-18 23:51:03.724][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 23:51:03.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:03.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:03.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:03.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:03.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:03.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:03.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:51:03.826][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:03.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:03.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:03.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:03.834][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:03.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:03.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:03.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:03.886][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:03.888][private$selectFields]
biodb.TRACE[2022-10-18 23:51:03.890][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:51:03.892][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:51:03.894][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:03.896][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:03.898][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:03.900][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:03.902][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:03.904][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:03.907][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:03.909][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:03.911][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:03.913][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:03.939][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:03.941][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:03.943][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:03.945][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:03.947][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:03.949][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 23:51:03.951][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:03.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:03.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:03.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:03.960][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:03.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:03.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:03.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:03.968][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:03.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:03.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:03.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:03.976][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-10-18 23:51:03.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:03.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:03.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:03.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:03.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:03.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:03.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:51:04.001][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.009][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.018][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:04.020][private$selectFields]
biodb.TRACE[2022-10-18 23:51:04.022][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:51:04.024][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:51:04.026][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:04.028][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.030][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.032][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.034][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.036][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.038][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.040][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.042][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.045][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:04.047][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:04.049][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.052][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.054][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.056][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.058][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 23:51:04.060][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.067][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.076][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.086][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-10-18 23:51:04.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:04.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:04.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:04.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:04.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:04.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:04.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:51:04.111][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.120][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.128][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:04.129][private$selectFields]
biodb.TRACE[2022-10-18 23:51:04.130][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:51:04.132][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:51:04.134][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:04.136][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.138][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.140][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.141][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.144][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.146][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.147][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.149][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.151][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:04.153][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:04.155][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.158][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.160][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.162][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.165][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 23:51:04.167][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.176][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.184][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:04.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.194][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-10-18 23:51:04.196][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 23:51:04.198][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 23:51:04.249][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 23:51:04.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 23:51:04.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 23:51:04.257][biodb::testThat]
biodb.INFO [2022-10-18 23:51:04.259][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2022-10-18 23:51:04.260][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:51:04.262][biodb::testThat]
biodb.TRACE[2022-10-18 23:51:04.268][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 23:51:04.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 23:51:04.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:51:04.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:51:04.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:51:04.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:51:04.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:51:04.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:51:04.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:51:04.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:51:04.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:04.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:51:04.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:51:04.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:04.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:51:04.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:04.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:04.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:04.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:04.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:04.350][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:04.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:04.592][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2022-10-18 23:51:04.600][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:04.602][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:04.606][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2022-10-18 23:51:09.522][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2022-10-18 23:51:16.216][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:51:16.233][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2022-10-18 23:51:16.352][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2022-10-18 23:51:16.933][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 23:51:16.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:16.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:16.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:16.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:16.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:16.955][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:16.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:51:16.960][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:16.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:16.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:16.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:16.970][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:16.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:16.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:16.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:16.980][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:16.982][private$selectFields]
biodb.TRACE[2022-10-18 23:51:16.984][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:51:16.986][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:51:16.988][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:16.990][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:16.993][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:16.995][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:16.997][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:16.999][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.002][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.004][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.006][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.008][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:17.010][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:17.012][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.015][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.018][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.020][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.022][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 23:51:17.024][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.033][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.042][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.051][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-10-18 23:51:17.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:17.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:17.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:17.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:17.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:17.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:17.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:51:17.077][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.087][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.096][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:17.098][private$selectFields]
biodb.TRACE[2022-10-18 23:51:17.101][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:51:17.103][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:51:17.106][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:17.109][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.111][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.113][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.116][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.119][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.121][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.123][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.126][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.128][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:17.130][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:17.132][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.135][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.137][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.139][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.141][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 23:51:17.143][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.152][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.164][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.174][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-10-18 23:51:17.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:17.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:17.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:17.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:17.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:17.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:17.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:51:17.198][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.207][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.215][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:17.217][private$selectFields]
biodb.TRACE[2022-10-18 23:51:17.219][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:51:17.221][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:51:17.223][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:17.225][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.227][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.229][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.231][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.233][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.236][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.238][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.240][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.242][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:17.243][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:51:17.245][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.248][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.250][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.252][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.254][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 23:51:17.256][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.264][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.275][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:17.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:17.284][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-10-18 23:51:17.286][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 23:51:17.288][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 23:51:17.331][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 23:51:17.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 23:51:17.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:17.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 23:51:17.342][biodb::testThat]
biodb.INFO [2022-10-18 23:51:17.344][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2022-10-18 23:51:17.346][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:51:17.348][biodb::testThat]
biodb.DEBUG[2022-10-18 23:51:17.353][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2022-10-18 23:51:17.355][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:51:17.359][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2022-10-18 23:51:17.362][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:51:17.364][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:51:17.366][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:51:17.368][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 23:51:17.370][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:51:17.372][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:51:17.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:17.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:17.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:17.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:17.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:17.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:17.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:17.432][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2022-10-18 23:51:17.438][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:17.441][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:17.446][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 23:51:18.093][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:18.096][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:18.098][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:18.101][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 23:51:18.949][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:18.951][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:18.954][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:18.957][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 23:51:19.616][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:19.618][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:19.620][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:19.623][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 23:51:20.350][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:20.353][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:20.354][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:20.356][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 23:51:20.986][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:20.988][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:20.990][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:20.992][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 23:51:21.740][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:21.742][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:21.744][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:21.747][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 23:51:22.380][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:22.381][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:22.383][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:22.385][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 23:51:23.280][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:23.282][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:23.284][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:23.287][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 23:51:23.898][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:23.900][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:23.902][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:23.904][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 23:51:24.744][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:24.746][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:24.748][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:24.751][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 23:51:25.394][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:25.395][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:25.397][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:25.399][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 23:51:26.145][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:26.147][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:26.149][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:26.152][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 23:51:26.777][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:26.779][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:26.781][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:26.783][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 23:51:27.530][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:27.533][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:27.535][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:27.538][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 23:51:28.183][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:28.186][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:28.188][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:28.190][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 23:51:28.968][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:28.970][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:28.972][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:28.975][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 23:51:29.593][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:29.595][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:29.597][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:29.600][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 23:51:30.581][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:30.583][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:30.585][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:30.588][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 23:51:31.219][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:31.221][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:31.223][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:31.225][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 23:51:32.041][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2022-10-18 23:51:32.107][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2022-10-18 23:51:32.116][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:51:32.145][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:51:32.148][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-10-18 23:51:32.151][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:32.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:32.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:32.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:32.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:32.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:32.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:51:32.174][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:32.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:32.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:32.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:32.182][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:32.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:32.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:32.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:32.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:32.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:32.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:32.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:32.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:32.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:32.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:32.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:32.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:32.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:32.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:32.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:32.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:32.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:32.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:32.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:32.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:32.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:32.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:32.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:32.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:32.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:32.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:32.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:51:32.237][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2022-10-18 23:51:32.239][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2022-10-18 23:51:32.252][biodb::testThat]
biodb.INFO [2022-10-18 23:51:32.254][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2022-10-18 23:51:32.256][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:51:32.258][biodb::testThat]
biodb.DEBUG[2022-10-18 23:51:32.274][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2022-10-18 23:51:32.276][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2022-10-18 23:51:32.278][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-10-18 23:51:32.281][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2022-10-18 23:51:32.283][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2022-10-18 23:51:32.285][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:51:32.287][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:51:32.289][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 23:51:32.291][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:51:32.292][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:51:32.299][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:32.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:32.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:32.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:32.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:32.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:32.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:32.320][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2022-10-18 23:51:32.326][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:32.328][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:32.330][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 23:51:32.949][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:32.951][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:32.953][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:32.955][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 23:51:33.671][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:33.673][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:33.675][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:33.678][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 23:51:34.305][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:34.307][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:34.309][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:34.311][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 23:51:35.369][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:35.372][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:35.374][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:35.376][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 23:51:36.000][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:36.002][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:36.004][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:36.006][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 23:51:36.867][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:36.869][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:36.871][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:36.873][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 23:51:37.512][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:37.514][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:37.516][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:37.519][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 23:51:38.372][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:38.374][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:38.377][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:38.379][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 23:51:39.002][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:39.004][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:39.006][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:39.008][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 23:51:39.730][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:39.732][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:39.734][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:39.737][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 23:51:40.332][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:40.334][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:40.336][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:40.337][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 23:51:41.178][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:41.179][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:41.182][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:41.184][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 23:51:41.818][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:41.819][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:41.821][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:41.824][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 23:51:42.541][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:42.543][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:42.545][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:42.548][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 23:51:43.176][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:43.178][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:43.181][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:43.183][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 23:51:44.033][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:44.035][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:44.037][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:44.039][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 23:51:44.627][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:44.629][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:44.631][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:44.634][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 23:51:45.468][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:45.470][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:45.472][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:45.474][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 23:51:46.095][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 23:51:46.097][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 23:51:46.099][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 23:51:46.102][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 23:51:47.055][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 23:51:47.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:47.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:47.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:47.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:47.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:47.075][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:47.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:47.079][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2022-10-18 23:51:47.085][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:47.087][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:47.090][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2022-10-18 23:51:47.759][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2022-10-18 23:51:48.445][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:51:48.461][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2022-10-18 23:51:48.485][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2022-10-18 23:51:48.507][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2022-10-18 23:51:48.517][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:51:48.549][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-10-18 23:51:48.552][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-10-18 23:51:48.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:48.557][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:48.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:48.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:48.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:48.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:48.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:51:48.576][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:48.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:48.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.584][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:48.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:48.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:48.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:48.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:51:48.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:48.639][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:48.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:48.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:48.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:48.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:48.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:51:48.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:48.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:48.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:48.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:48.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:51:48.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:51:48.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:51:48.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:51:48.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.709][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 23:51:48.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 23:51:48.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.717][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 23:51:48.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 23:51:48.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.732][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:51:48.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:51:48.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.741][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:51:48.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:51:48.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.755][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:51:48.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:51:48.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.762][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:51:48.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:51:48.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.774][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:51:48.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:51:48.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.782][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:51:48.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:51:48.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.795][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 23:51:48.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:51:48.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.802][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 23:51:48.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:51:48.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.815][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:51:48.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:51:48.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.822][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:51:48.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:51:48.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.833][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:51:48.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:51:48.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.841][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:51:48.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:51:48.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.854][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 23:51:48.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:51:48.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.863][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 23:51:48.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:51:48.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:51:48.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:51:48.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.879][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:51:48.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:51:48.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.886][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 23:51:48.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:51:48.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.900][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:51:48.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:51:48.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.907][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:51:48.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:51:48.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.914][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:51:48.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:51:48.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.922][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:51:48.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:51:48.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.930][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:51:48.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:51:48.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.943][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:48.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:48.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.952][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:48.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:48.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:48.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:48.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.966][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:48.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:51:48.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:48.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:48.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:48.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:48.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:48.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:48.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:48.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:48.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:49.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:49.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:49.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:49.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:49.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:49.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:49.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:49.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:49.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:49.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:49.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:49.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:49.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:49.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:49.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:49.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:49.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:49.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:49.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:49.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:49.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:49.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:49.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:49.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:49.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:49.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:49.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:49.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:49.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:49.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:49.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:49.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:51:49.064][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2022-10-18 23:51:49.066][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2022-10-18 23:51:49.068][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2022-10-18 23:51:49.091][biodb::testThat]
biodb.INFO [2022-10-18 23:51:49.093][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2022-10-18 23:51:49.095][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:51:49.098][biodb::testThat]
biodb.INFO [2022-10-18 23:51:49.136][biodb::testThat]
biodb.INFO [2022-10-18 23:51:49.138][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2022-10-18 23:51:49.140][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:51:49.142][biodb::testThat]
biodb.INFO [2022-10-18 23:51:49.153][biodb::testThat]
biodb.INFO [2022-10-18 23:51:49.156][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2022-10-18 23:51:49.158][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:51:49.160][biodb::testThat]
biodb.DEBUG[2022-10-18 23:51:49.335][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2022-10-18 23:51:49.340][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:49.342][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:49.345][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2022-10-18 23:51:54.157][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2022-10-18 23:52:01.231][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:52:01.248][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2022-10-18 23:52:01.375][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2022-10-18 23:52:01.885][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:01.887][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:01.889][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:01.891][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:01.893][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:01.896][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:01.898][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:01.900][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 23:52:01.903][biodb::testThat]
biodb.INFO [2022-10-18 23:52:01.905][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2022-10-18 23:52:01.907][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:52:01.908][biodb::testThat]
biodb.ERROR[2022-10-18 23:52:01.931][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2022-10-18 23:52:01.959][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2022-10-18 23:52:01.977][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 23:52:01.979][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-10-18 23:52:01.982][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-10-18 23:52:01.984][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 23:52:01.986][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:01.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:01.989][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:01.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:01.993][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:01.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-10-18 23:52:02.015][biodb::testContext]
biodb.INFO [2022-10-18 23:52:02.017][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 23:52:02.019][biodb::testContext] Test context - Web services tests
biodb.INFO [2022-10-18 23:52:02.021][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 23:52:02.023][biodb::testContext]
biodb.INFO [2022-10-18 23:52:02.034][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 23:52:02.037][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 23:52:02.046][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:52:02.048][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 23:52:02.050][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 23:52:02.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.058][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 23:52:02.059][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 23:52:02.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.067][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 23:52:02.069][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 23:52:02.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.076][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 23:52:02.077][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 23:52:02.080][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 23:52:02.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.088][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 23:52:02.089][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 23:52:02.090][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 23:52:02.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.096][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 23:52:02.098][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 23:52:02.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.104][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 23:52:02.106][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 23:52:02.108][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 23:52:02.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.116][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 23:52:02.118][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 23:52:02.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.126][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 23:52:02.128][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 23:52:02.130][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 23:52:02.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.138][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 23:52:02.140][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 23:52:02.142][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 23:52:02.145][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 23:52:02.147][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 23:52:02.149][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 23:52:02.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.154][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[2022-10-18 23:52:02.155][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 23:52:02.156][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 23:52:02.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.163][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 23:52:02.165][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 23:52:02.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.171][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 23:52:02.173][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 23:52:02.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.179][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 23:52:02.181][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 23:52:02.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.187][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 23:52:02.189][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 23:52:02.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.197][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 23:52:02.199][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 23:52:02.210][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-10-18 23:52:02.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.217][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 23:52:02.219][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 23:52:02.221][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 23:52:02.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.229][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 23:52:02.233][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:02.235][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-18 23:52:02.237][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:02.239][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:52:02.241][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:02.242][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:52:02.244][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:02.246][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:52:02.248][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 23:52:02.250][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:52:02.252][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:02.254][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 23:52:02.256][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:52:02.258][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:02.259][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:02.261][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:52:02.261][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:52:02.261][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 23:52:02.261][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 23:52:02.261][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 23:52:02.263][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:52:02.265][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:02.266][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:02.268][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:52:02.270][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:02.272][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:02.274][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:52:02.275][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:02.277][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:52:02.278][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:52:02.280][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:02.282][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:02.285][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 23:52:02.289][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:02.291][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 23:52:02.293][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:02.295][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:52:02.298][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:02.300][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:52:02.302][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:02.304][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:52:02.306][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 23:52:02.309][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:52:02.311][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:02.312][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 23:52:02.314][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:52:02.315][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:02.317][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:02.318][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:52:02.318][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:52:02.318][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 23:52:02.318][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 23:52:02.318][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 23:52:02.319][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:52:02.321][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:02.322][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:02.323][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:52:02.325][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:02.326][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:02.328][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:52:02.329][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:02.331][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:52:02.332][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:52:02.334][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:02.335][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:02.338][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 23:52:02.340][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:02.342][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-18 23:52:02.344][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:02.346][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:52:02.348][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:02.349][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:52:02.351][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:02.352][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:52:02.354][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 23:52:02.357][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:52:02.358][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:02.359][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 23:52:02.361][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:52:02.362][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:02.363][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:02.364][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:02.366][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:52:02.368][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:02.369][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:02.371][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:52:02.373][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:02.375][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:02.377][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:52:02.379][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:02.381][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:52:02.383][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:52:02.385][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:02.387][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:02.389][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 23:52:02.412][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:02.414][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 23:52:02.416][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:02.418][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:52:02.420][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:02.422][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:52:02.424][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:02.425][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:52:02.427][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 23:52:02.429][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:52:02.430][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:02.432][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 23:52:02.435][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:52:02.437][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:02.439][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:02.441][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:02.442][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:52:02.444][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:02.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:02.448][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:52:02.450][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:02.451][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:02.453][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:52:02.455][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:02.457][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:52:02.459][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:52:02.461][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:02.462][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:02.465][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:52:02.466][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.477][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[2022-10-18 23:52:02.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.509][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[2022-10-18 23:52:02.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.519][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[2022-10-18 23:52:02.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.526][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.DEBUG[2022-10-18 23:52:02.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.561][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[2022-10-18 23:52:02.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.593][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[2022-10-18 23:52:02.595][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 23:52:02.598][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 23:52:02.601][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 23:52:02.604][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 23:52:02.607][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 23:52:02.609][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 23:52:02.610][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 23:52:02.612][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 23:52:02.614][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 23:52:02.617][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 23:52:02.620][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 23:52:02.623][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 23:52:02.625][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 23:52:02.628][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 23:52:02.631][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 23:52:02.634][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 23:52:02.637][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 23:52:02.640][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 23:52:02.642][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 23:52:02.644][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 23:52:02.647][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 23:52:02.650][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 23:52:02.652][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 23:52:02.655][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 23:52:02.659][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 23:52:02.662][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 23:52:02.665][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 23:52:02.668][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 23:52:02.671][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 23:52:02.674][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 23:52:02.676][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 23:52:02.679][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 23:52:02.683][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 23:52:02.685][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 23:52:02.688][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 23:52:02.691][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 23:52:02.695][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 23:52:02.698][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 23:52:02.701][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 23:52:02.704][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 23:52:02.707][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 23:52:02.710][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 23:52:02.713][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 23:52:02.716][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 23:52:02.719][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 23:52:02.722][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 23:52:02.724][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 23:52:02.726][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 23:52:02.728][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 23:52:02.731][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 23:52:02.734][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 23:52:02.737][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 23:52:02.739][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 23:52:02.742][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 23:52:02.746][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 23:52:02.749][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 23:52:02.752][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 23:52:02.755][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 23:52:02.757][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 23:52:02.759][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 23:52:02.760][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 23:52:02.762][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 23:52:02.765][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 23:52:02.768][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 23:52:02.771][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 23:52:02.774][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 23:52:02.777][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 23:52:02.778][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 23:52:02.781][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 23:52:02.784][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 23:52:02.787][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 23:52:02.791][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 23:52:02.794][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 23:52:02.797][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 23:52:02.800][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 23:52:02.804][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 23:52:02.807][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 23:52:02.810][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 23:52:02.813][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 23:52:02.816][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 23:52:02.818][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 23:52:02.820][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 23:52:02.822][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 23:52:02.825][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 23:52:02.828][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 23:52:02.830][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:52:02.832][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.836][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:02.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:02.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:02.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:02.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:02.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:02.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:02.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:02.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:02.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:02.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:02.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:02.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:02.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:02.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:02.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:02.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:02.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:02.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:02.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:02.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:02.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:02.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:02.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:02.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:02.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:02.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:02.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:02.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:02.997][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[2022-10-18 23:52:02.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:03.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:03.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:03.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:03.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:03.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:03.008][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[2022-10-18 23:52:03.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:03.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:03.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:03.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:03.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:03.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:03.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:03.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:03.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:03.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:03.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:03.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:03.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:03.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:03.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:03.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:03.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:03.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:03.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:03.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:03.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:03.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:03.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:03.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:03.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:03.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:03.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:03.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:03.059][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-10-18 23:52:03.062][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 23:52:03.066][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:03.069][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 23:52:03.071][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:03.073][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:52:03.076][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:03.078][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:52:03.080][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:03.082][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:52:03.084][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 23:52:03.086][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:52:03.088][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:03.090][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-10-18 23:52:03.092][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:52:03.094][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-10-18 23:52:03.094][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-10-18 23:52:03.094][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-10-18 23:52:03.094][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-10-18 23:52:03.094][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-10-18 23:52:03.094][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-10-18 23:52:03.094][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-10-18 23:52:03.094][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-10-18 23:52:03.094][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-10-18 23:52:03.096][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:03.098][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:52:03.098][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:52:03.100][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:52:03.101][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:03.103][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:03.105][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:52:03.106][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:03.107][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:03.109][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:52:03.110][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 23:52:03.110][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-10-18 23:52:03.111][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:52:03.113][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:52:03.115][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:03.117][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:03.120][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-10-18 23:52:03.123][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 23:52:03.130][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 23:52:03.132][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-10-18 23:52:03.134][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 23:52:03.137][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-10-18 23:52:03.140][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-10-18 23:52:03.142][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-10-18 23:52:03.145][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-10-18 23:52:03.147][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-10-18 23:52:03.151][biodb::testThat]
biodb.INFO [2022-10-18 23:52:03.153][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2022-10-18 23:52:03.155][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:52:03.157][biodb::testThat]
biodb.DEBUG[2022-10-18 23:52:03.300][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[2022-10-18 23:52:03.307][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:52:03.308][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:52:03.311][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2022-10-18 23:52:03.996][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2022-10-18 23:52:04.686][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:52:04.698][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2022-10-18 23:52:04.719][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2022-10-18 23:52:04.898][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2022-10-18 23:52:04.905][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:52:04.907][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:52:04.911][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2022-10-18 23:52:05.605][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2022-10-18 23:52:06.296][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:52:06.310][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2022-10-18 23:52:06.334][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2022-10-18 23:52:06.354][biodb::testThat]
biodb.INFO [2022-10-18 23:52:06.357][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2022-10-18 23:52:06.358][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:52:06.360][biodb::testThat]
biodb.INFO [2022-10-18 23:52:06.404][biodb::testThat]
biodb.INFO [2022-10-18 23:52:06.406][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2022-10-18 23:52:06.407][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:52:06.409][biodb::testThat]
biodb.DEBUG[2022-10-18 23:52:06.558][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[2022-10-18 23:52:06.564][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:52:06.566][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:52:06.568][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2022-10-18 23:52:07.064][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2022-10-18 23:52:07.618][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:52:07.634][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2022-10-18 23:52:07.659][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2022-10-18 23:52:07.833][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2022-10-18 23:52:07.840][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:52:07.843][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2022-10-18 23:52:07.846][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:52:07.848][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2022-10-18 23:52:08.021][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2022-10-18 23:52:08.028][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:52:08.030][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:52:08.034][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2022-10-18 23:52:08.537][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2022-10-18 23:52:09.063][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:52:09.080][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2022-10-18 23:52:09.103][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2022-10-18 23:52:09.294][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[2022-10-18 23:52:09.300][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:52:09.302][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:52:09.306][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2022-10-18 23:52:10.669][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2022-10-18 23:52:12.349][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:52:12.364][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2022-10-18 23:52:12.392][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2022-10-18 23:52:12.627][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2022-10-18 23:52:12.635][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:52:12.637][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:52:12.642][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2022-10-18 23:52:13.978][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2022-10-18 23:52:15.677][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:52:15.692][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2022-10-18 23:52:15.754][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2022-10-18 23:52:15.834][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 23:52:15.837][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-10-18 23:52:15.839][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-10-18 23:52:15.840][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 23:52:15.842][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:15.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:15.846][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:15.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:15.848][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:15.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-10-18 23:52:15.855][biodb::testContext]
biodb.INFO [2022-10-18 23:52:15.857][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 23:52:15.859][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2022-10-18 23:52:15.862][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 23:52:15.864][biodb::testContext]
biodb.INFO [2022-10-18 23:52:15.873][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 23:52:15.877][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 23:52:15.883][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:52:15.886][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 23:52:15.889][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 23:52:15.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:15.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:15.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:15.897][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 23:52:15.899][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 23:52:15.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:15.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:15.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:15.906][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 23:52:15.908][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 23:52:15.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:15.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:15.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:15.915][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 23:52:15.917][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 23:52:15.918][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 23:52:15.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:15.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:15.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:15.926][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 23:52:15.928][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 23:52:15.930][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 23:52:15.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:15.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:15.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:15.937][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 23:52:15.939][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 23:52:15.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:15.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:15.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:15.947][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 23:52:15.949][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 23:52:15.951][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 23:52:15.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:15.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:15.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:15.959][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 23:52:15.961][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 23:52:15.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:15.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:15.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:15.969][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 23:52:15.971][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 23:52:15.973][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 23:52:15.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:15.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:15.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:15.981][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 23:52:15.983][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 23:52:15.985][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 23:52:15.986][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 23:52:15.988][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 23:52:15.990][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 23:52:15.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:15.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:15.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:15.999][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 23:52:16.001][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 23:52:16.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.008][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 23:52:16.010][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 23:52:16.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.019][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 23:52:16.021][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 23:52:16.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.029][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 23:52:16.032][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 23:52:16.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.040][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 23:52:16.042][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 23:52:16.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.050][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 23:52:16.053][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 23:52:16.065][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-10-18 23:52:16.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.072][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 23:52:16.074][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 23:52:16.076][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 23:52:16.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.082][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 23:52:16.086][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:16.088][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-18 23:52:16.090][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.092][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:52:16.094][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.096][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:52:16.098][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:16.100][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:52:16.102][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 23:52:16.104][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:52:16.106][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.108][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 23:52:16.109][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:52:16.111][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:16.113][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.114][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:52:16.114][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:52:16.114][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 23:52:16.114][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 23:52:16.114][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 23:52:16.116][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:52:16.117][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:16.118][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:16.120][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:52:16.122][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:16.124][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:16.126][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:52:16.128][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:16.130][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:52:16.132][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:52:16.134][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:16.136][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:16.139][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 23:52:16.143][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:16.145][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 23:52:16.147][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.149][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:52:16.152][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.154][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:52:16.156][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:16.158][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:52:16.160][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 23:52:16.162][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:52:16.164][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.167][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 23:52:16.169][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:52:16.171][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:16.173][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.175][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:52:16.175][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:52:16.175][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 23:52:16.175][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 23:52:16.175][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 23:52:16.177][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:52:16.179][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:16.180][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:16.182][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:52:16.184][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:16.186][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:16.188][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:52:16.190][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:16.192][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:52:16.194][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:52:16.196][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:16.198][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:16.201][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 23:52:16.204][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.207][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-18 23:52:16.209][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.211][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:52:16.213][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.215][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:52:16.217][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:16.219][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:52:16.221][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 23:52:16.223][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:52:16.225][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:16.227][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 23:52:16.230][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:52:16.232][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:16.235][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.237][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:16.239][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:52:16.241][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:16.243][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:16.245][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:52:16.246][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:16.248][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:16.249][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:52:16.250][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:16.251][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:52:16.252][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:52:16.253][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:16.255][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:16.258][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 23:52:16.262][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.264][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 23:52:16.266][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.269][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:52:16.271][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.273][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:52:16.275][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:16.277][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:52:16.279][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 23:52:16.282][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:52:16.284][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:16.286][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 23:52:16.289][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:52:16.291][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:16.293][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.295][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:16.297][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:52:16.299][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:16.301][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:16.303][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:52:16.305][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:16.307][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:16.309][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:52:16.311][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:16.313][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:52:16.314][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:52:16.316][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:16.319][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:16.322][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:52:16.324][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.372][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[2022-10-18 23:52:16.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.389][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[2022-10-18 23:52:16.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.466][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[2022-10-18 23:52:16.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.491][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 23:52:16.494][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 23:52:16.497][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 23:52:16.500][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 23:52:16.502][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 23:52:16.505][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 23:52:16.508][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 23:52:16.510][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 23:52:16.512][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 23:52:16.515][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 23:52:16.518][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 23:52:16.520][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 23:52:16.523][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 23:52:16.526][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 23:52:16.529][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 23:52:16.531][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 23:52:16.534][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 23:52:16.537][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 23:52:16.540][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 23:52:16.542][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 23:52:16.545][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 23:52:16.548][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 23:52:16.551][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 23:52:16.554][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 23:52:16.557][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 23:52:16.560][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 23:52:16.563][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 23:52:16.566][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 23:52:16.569][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 23:52:16.572][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 23:52:16.575][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 23:52:16.578][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 23:52:16.582][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 23:52:16.585][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 23:52:16.587][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 23:52:16.590][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 23:52:16.593][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 23:52:16.596][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 23:52:16.598][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 23:52:16.601][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 23:52:16.604][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 23:52:16.606][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 23:52:16.609][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 23:52:16.611][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 23:52:16.612][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 23:52:16.615][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 23:52:16.618][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 23:52:16.621][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 23:52:16.624][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 23:52:16.626][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 23:52:16.629][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 23:52:16.632][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 23:52:16.634][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 23:52:16.637][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 23:52:16.640][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 23:52:16.642][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 23:52:16.645][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 23:52:16.648][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 23:52:16.651][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 23:52:16.653][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 23:52:16.656][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 23:52:16.659][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 23:52:16.660][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 23:52:16.663][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 23:52:16.666][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 23:52:16.667][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 23:52:16.669][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 23:52:16.672][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 23:52:16.675][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 23:52:16.678][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 23:52:16.681][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 23:52:16.683][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 23:52:16.686][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 23:52:16.688][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 23:52:16.691][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 23:52:16.693][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 23:52:16.695][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 23:52:16.698][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 23:52:16.701][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 23:52:16.704][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 23:52:16.707][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 23:52:16.710][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 23:52:16.712][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 23:52:16.714][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 23:52:16.717][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 23:52:16.719][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:52:16.721][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.724][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:16.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:16.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:16.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:16.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:16.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:16.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:16.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:16.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:16.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:16.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:16.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:16.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:16.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:16.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:16.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:16.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.813][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[2022-10-18 23:52:16.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:16.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:16.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:16.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:16.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:16.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:16.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.851][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[2022-10-18 23:52:16.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:16.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:16.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.862][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[2022-10-18 23:52:16.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:16.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:16.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.874][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[2022-10-18 23:52:16.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:16.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:16.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:16.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:16.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:16.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:16.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:52:16.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:16.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:16.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:16.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:16.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:16.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:16.924][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-10-18 23:52:16.926][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 23:52:16.929][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:16.930][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 23:52:16.931][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.933][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:52:16.935][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.937][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:52:16.939][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.942][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:52:16.944][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 23:52:16.946][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:52:16.948][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:16.950][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-10-18 23:52:16.952][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:52:16.954][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-10-18 23:52:16.954][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-10-18 23:52:16.954][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-10-18 23:52:16.954][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-10-18 23:52:16.954][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-10-18 23:52:16.954][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-10-18 23:52:16.954][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-10-18 23:52:16.954][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-10-18 23:52:16.954][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-10-18 23:52:16.957][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 23:52:16.959][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:52:16.959][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:52:16.961][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:52:16.963][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:16.964][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:16.986][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:52:16.988][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:52:16.990][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:52:16.992][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:52:16.993][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 23:52:16.993][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-10-18 23:52:16.995][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:52:16.996][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:52:16.998][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 23:52:17.000][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:52:17.002][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-10-18 23:52:17.004][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 23:52:17.011][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 23:52:17.013][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-10-18 23:52:17.016][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 23:52:17.018][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-10-18 23:52:17.020][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-10-18 23:52:17.021][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-10-18 23:52:17.023][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-10-18 23:52:17.025][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-10-18 23:52:17.027][biodb::testThat]
biodb.INFO [2022-10-18 23:52:17.029][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2022-10-18 23:52:17.030][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:52:17.032][biodb::testThat]
biodb.DEBUG[2022-10-18 23:52:17.188][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[2022-10-18 23:52:17.196][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:52:17.198][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2022-10-18 23:52:17.200][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:52:17.253][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2022-10-18 23:52:18.432][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2022-10-18 23:52:18.434][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-10-18 23:52:18.436][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2022-10-18 23:52:18.439][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2022-10-18 23:52:18.441][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:52:18.466][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:52:18.467][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 23:52:18.469][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:52:18.470][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:52:18.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:52:18.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:18.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:18.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:18.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:18.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:18.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:18.498][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2022-10-18 23:52:18.503][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:52:18.505][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:52:18.507][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2022-10-18 23:52:19.184][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.DEBUG[2022-10-18 23:52:19.863][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:52:19.880][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.content"
biodb.TRACE[2022-10-18 23:52:19.904][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.request"
biodb.DEBUG[2022-10-18 23:52:19.913][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:52:19.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:19.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:19.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:19.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:19.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:19.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:52:19.934][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2022-10-18 23:52:19.940][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:52:19.941][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:52:19.943][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2022-10-18 23:52:20.609][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2022-10-18 23:52:21.259][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:52:21.270][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2022-10-18 23:52:21.290][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.TRACE[2022-10-18 23:52:21.309][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv"
biodb.DEBUG[2022-10-18 23:52:21.318][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:52:21.346][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-10-18 23:52:21.349][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-10-18 23:52:21.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:52:21.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:21.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:21.366][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:21.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:21.369][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:21.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:52:21.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:21.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:21.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:21.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:21.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:52:21.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:52:21.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:52:21.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:52:21.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.412][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 23:52:21.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 23:52:21.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.420][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:52:21.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:52:21.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.427][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:21.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:21.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.436][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:21.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:21.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.449][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:21.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:21.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.458][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:21.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:21.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.472][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 23:52:21.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:21.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.481][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 23:52:21.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:21.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.494][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:52:21.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:52:21.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.503][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:52:21.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:52:21.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.517][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:21.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:21.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.568][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 23:52:21.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.576][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 23:52:21.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.583][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:21.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:21.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.599][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 23:52:21.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.612][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:21.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.620][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:21.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.627][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:21.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.634][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:21.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:21.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.657][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:21.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:21.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.665][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:21.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:21.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:21.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:21.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.679][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:21.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:21.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:21.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:21.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:21.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:21.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:21.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:21.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:52:21.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:52:21.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:21.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:21.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:21.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:21.731][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:21.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:52:21.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:21.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:21.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:21.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:21.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:52:21.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:52:21.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:52:21.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:52:21.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.783][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 23:52:21.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 23:52:21.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.792][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:52:21.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:52:21.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.800][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:21.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:21.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.808][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:21.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:21.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.822][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:21.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:21.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.830][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:21.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:21.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.844][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 23:52:21.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:21.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.851][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 23:52:21.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:21.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.865][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:52:21.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:52:21.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.873][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:52:21.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:52:21.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.885][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:21.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.893][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:21.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.906][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 23:52:21.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.912][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 23:52:21.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.919][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:21.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.925][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:21.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.933][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 23:52:21.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:21.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.946][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:21.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:21.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.954][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:21.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:21.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:21.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:21.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.969][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:21.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:21.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:21.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:21.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:21.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:21.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:21.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:21.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:21.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:21.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:22.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:22.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:22.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:22.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:22.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:22.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:22.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:22.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:22.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:22.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:22.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:22.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:52:22.055][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2022-10-18 23:52:22.059][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 23:52:22.062][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:52:22.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:22.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:22.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:22.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:22.077][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:22.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:52:22.083][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 23:52:22.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 23:52:22.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.090][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 23:52:22.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 23:52:22.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.099][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 23:52:22.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 23:52:22.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.108][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 23:52:22.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 23:52:22.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.136][private$selectFields] Fields none
biodb.TRACE[2022-10-18 23:52:22.137][private$selectFields]
biodb.TRACE[2022-10-18 23:52:22.138][private$selectFields] Fields is null: TRUE
biodb.TRACE[2022-10-18 23:52:22.139][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:52:22.141][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:52:22.142][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:22.143][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:22.145][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.148][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.150][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.152][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.154][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.156][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.158][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.161][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.163][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.164][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.166][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.168][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.170][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.172][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.175][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.177][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.179][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.181][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.183][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:52:22.185][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:52:22.187][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.189][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.191][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:22.193][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:22.195][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.196][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.198][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.199][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.201][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.203][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.205][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:22.207][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:22.209][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.211][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.213][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.214][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.216][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.217][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.218][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.220][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.222][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.224][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.226][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.228][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.230][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.232][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.234][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.236][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.238][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.240][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.243][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:52:22.245][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:52:22.247][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.248][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.250][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:22.251][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:22.253][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.255][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.257][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.259][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.261][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.263][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.265][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:52:22.267][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:52:22.269][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:22.271][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:22.273][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.275][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.277][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.279][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.281][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.283][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.285][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.287][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.289][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.290][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.292][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.294][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.296][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.299][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.301][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.303][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.306][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.309][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.311][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:52:22.314][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:52:22.317][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.319][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.321][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:22.322][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:22.324][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.326][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.327][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.329][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.331][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.333][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.335][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2022-10-18 23:52:22.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:22.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:22.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:22.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:22.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:22.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:22.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.382][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.388][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.396][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.404][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.413][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.420][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.453][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:52:22.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:52:22.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.459][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:52:22.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:52:22.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.467][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:52:22.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:52:22.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.474][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:22.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:22.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.483][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:22.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:22.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:22.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:22.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.500][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.508][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.517][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.539][private$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[2022-10-18 23:52:22.541][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:52:22.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:22.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:22.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:22.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:22.559][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:22.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:52:22.565][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 23:52:22.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 23:52:22.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.573][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 23:52:22.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 23:52:22.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.581][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 23:52:22.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 23:52:22.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.591][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 23:52:22.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 23:52:22.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.598][private$selectFields] Fields none
biodb.TRACE[2022-10-18 23:52:22.600][private$selectFields]
biodb.TRACE[2022-10-18 23:52:22.602][private$selectFields] Fields is null: TRUE
biodb.TRACE[2022-10-18 23:52:22.603][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:52:22.605][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:52:22.606][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:22.608][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:22.610][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.611][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.613][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.615][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.617][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.619][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.621][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.623][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.625][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.627][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.628][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.629][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.631][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.633][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.635][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.637][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.639][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.641][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.643][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:52:22.645][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:52:22.647][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.649][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.651][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:22.653][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:22.655][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.656][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.658][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.661][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.663][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.664][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.666][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:22.667][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:22.668][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.670][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.672][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.674][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.676][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.677][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.679][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.680][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.682][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.684][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.686][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.689][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.691][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.749][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.751][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.753][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.755][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.758][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.760][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:52:22.762][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:52:22.764][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.765][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.767][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:22.769][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:22.770][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.772][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.774][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.776][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.777][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.779][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.780][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:52:22.781][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-10-18 23:52:22.784][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:22.786][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:22.788][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.790][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.792][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.794][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.796][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.797][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.799][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.801][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.803][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.805][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.807][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.809][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.811][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.812][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.814][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.815][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.816][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.818][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.820][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:52:22.822][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:52:22.824][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.825][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.827][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:22.829][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:22.831][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.832][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.834][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.836][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.838][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.839][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.840][private$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[2022-10-18 23:52:22.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:22.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:22.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:22.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:22.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:52:22.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:52:22.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.879][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:52:22.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.886][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.893][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.899][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 23:52:22.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.905][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.910][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.916][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 23:52:22.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.928][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:52:22.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.943][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:52:22.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:52:22.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.948][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:52:22.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:52:22.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.954][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:52:22.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:52:22.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.962][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:22.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:22.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:22.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:22.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.973][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:52:22.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:52:22.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.981][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.987][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:22.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:22.996][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:22.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 23:52:23.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:52:23.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:52:23.009][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2022-10-18 23:52:23.012][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 23:52:23.014][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2022-10-18 23:52:23.020][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 23:52:23.022][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-10-18 23:52:23.025][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-10-18 23:52:23.027][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 23:52:23.028][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:52:23.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:52:23.032][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:52:23.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:52:23.036][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:52:23.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 170 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 170 ]
> 
> proc.time()
   user  system elapsed 
 39.194   2.204 144.740

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn3.8650.6774.640
LipidmapsStructureEntry0.8040.0150.846