Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:07:30 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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 machv2


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? here 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 179/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.0.1  (landing page)
Pierrick Roger
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_14
git_last_commit: bda9e29
git_last_commit_date: 2021-10-27 16:13:11 -0500 (Wed, 27 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: biodbLipidmaps
Version: 1.0.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.0.1.tar.gz
StartedAt: 2022-01-13 10:39:10 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 10:42:25 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 194.8 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbLipidmaps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.0.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

biodbLipidmaps.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 [2022-01-13 10:40:15.450][biodb::testContext] 
biodb.INFO [2022-01-13 10:40:15.466][biodb::testContext] ********************************************************************************
biodb.INFO [2022-01-13 10:40:15.467][biodb::testContext] Test context - Generic tests
biodb.INFO [2022-01-13 10:40:15.469][biodb::testContext] ********************************************************************************
biodb.INFO [2022-01-13 10:40:15.471][biodb::testContext] 
biodb.INFO [2022-01-13 10:40:15.501][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-01-13 10:40:15.505][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-01-13 10:40:15.522][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-01-13 10:40:15.524][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-01-13 10:40:15.526][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-01-13 10:40:15.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:15.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:15.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:15.534][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-01-13 10:40:15.580][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-01-13 10:40:15.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:15.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:15.586][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[2022-01-13 10:40:15.587][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-01-13 10:40:15.590][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-01-13 10:40:15.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:15.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:15.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:15.597][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-01-13 10:40:15.599][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-01-13 10:40:15.602][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-01-13 10:40:15.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:15.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:15.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:15.610][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-01-13 10:40:15.613][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-01-13 10:40:15.615][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-01-13 10:40:15.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:15.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:15.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:15.623][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-01-13 10:40:15.626][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-01-13 10:40:15.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:15.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:15.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:15.634][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-01-13 10:40:15.637][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-01-13 10:40:15.639][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-01-13 10:40:15.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:15.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:15.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:15.646][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-01-13 10:40:15.649][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-01-13 10:40:15.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:15.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:15.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:15.656][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-01-13 10:40:15.658][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-01-13 10:40:15.660][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-01-13 10:40:15.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:15.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:15.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:15.668][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-01-13 10:40:15.670][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-01-13 10:40:15.672][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-01-13 10:40:15.674][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-01-13 10:40:15.677][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-01-13 10:40:15.679][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-01-13 10:40:15.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:15.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:15.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:15.687][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-01-13 10:40:15.689][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-01-13 10:40:15.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:15.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:15.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:15.698][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-01-13 10:40:15.700][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-01-13 10:40:15.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:15.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:15.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:15.708][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-01-13 10:40:15.710][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-01-13 10:40:15.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:15.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:15.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:15.715][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-01-13 10:40:15.718][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-01-13 10:40:15.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:15.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:15.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:15.725][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-01-13 10:40:15.727][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-01-13 10:40:15.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:15.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:15.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:15.734][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-01-13 10:40:15.736][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-01-13 10:40:15.746][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-01-13 10:40:15.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:15.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:15.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:15.754][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-01-13 10:40:15.756][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-01-13 10:40:15.758][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-01-13 10:40:15.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:15.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:15.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:15.770][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-01-13 10:40:15.858][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-01-13 10:40:15.885][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-01-13 10:40:15.887][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:15.888][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-13 10:40:15.890][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:15.892][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-13 10:40:15.894][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-13 10:40:15.896][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-13 10:40:15.898][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-01-13 10:40:15.899][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-13 10:40:15.901][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:15.903][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-01-13 10:40:15.905][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-13 10:40:15.907][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:40:15.908][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:15.910][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-01-13 10:40:15.910][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-01-13 10:40:15.910][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-01-13 10:40:15.910][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-01-13 10:40:15.910][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-01-13 10:40:15.911][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-13 10:40:15.912][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:40:15.914][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:40:15.916][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-13 10:40:15.917][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:40:15.919][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:40:15.920][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-13 10:40:15.922][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:40:15.923][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-13 10:40:15.925][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-13 10:40:15.927][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-13 10:40:15.929][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:40:15.931][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-01-13 10:40:15.933][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-01-13 10:40:15.935][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-01-13 10:40:15.937][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:15.939][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-13 10:40:15.941][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:15.942][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-13 10:40:15.944][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-13 10:40:15.945][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-13 10:40:15.947][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-01-13 10:40:15.948][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-13 10:40:15.950][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:15.952][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-01-13 10:40:15.954][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-13 10:40:15.955][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:40:15.957][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:15.958][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-01-13 10:40:15.958][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-01-13 10:40:15.958][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-01-13 10:40:15.958][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-01-13 10:40:15.958][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-01-13 10:40:15.959][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-13 10:40:15.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:40:15.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:40:15.963][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-13 10:40:15.965][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:40:15.966][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:40:15.967][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-13 10:40:15.969][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:40:15.971][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-13 10:40:15.973][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-13 10:40:15.974][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-13 10:40:15.976][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:40:15.979][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-01-13 10:40:15.982][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:15.984][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-01-13 10:40:15.986][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:15.988][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-13 10:40:15.990][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:15.991][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-13 10:40:15.992][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-13 10:40:15.993][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-13 10:40:15.995][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-01-13 10:40:15.997][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-13 10:40:15.998][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-01-13 10:40:16.000][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-01-13 10:40:16.002][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-13 10:40:16.004][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:40:16.006][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:16.008][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:40:16.010][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-13 10:40:16.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:40:16.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:40:16.014][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-13 10:40:16.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:40:16.017][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:40:16.019][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-13 10:40:16.020][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:40:16.022][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-13 10:40:16.024][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-13 10:40:16.026][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-13 10:40:16.027][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:40:16.029][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-01-13 10:40:16.033][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:16.035][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-01-13 10:40:16.037][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:16.038][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-13 10:40:16.039][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:16.041][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-13 10:40:16.043][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-13 10:40:16.044][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-13 10:40:16.046][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-01-13 10:40:16.048][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-13 10:40:16.050][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-01-13 10:40:16.052][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-01-13 10:40:16.054][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-13 10:40:16.056][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:40:16.058][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:16.060][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:40:16.062][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-13 10:40:16.064][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:40:16.065][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:40:16.067][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-13 10:40:16.068][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:40:16.070][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:40:16.072][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-13 10:40:16.074][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:40:16.076][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-13 10:40:16.077][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-13 10:40:16.079][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-13 10:40:16.080][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:40:16.088][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-01-13 10:40:16.090][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.196][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.DEBUG[2022-01-13 10:40:16.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.222][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-01-13 10:40:16.232][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-01-13 10:40:16.235][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-01-13 10:40:16.238][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-01-13 10:40:16.241][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-01-13 10:40:16.244][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-01-13 10:40:16.246][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-01-13 10:40:16.248][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-01-13 10:40:16.250][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-01-13 10:40:16.253][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-01-13 10:40:16.255][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-01-13 10:40:16.258][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-01-13 10:40:16.261][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-01-13 10:40:16.270][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-01-13 10:40:16.273][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-01-13 10:40:16.275][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-01-13 10:40:16.278][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-01-13 10:40:16.281][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-01-13 10:40:16.284][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-01-13 10:40:16.287][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-01-13 10:40:16.290][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-01-13 10:40:16.292][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-01-13 10:40:16.295][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-01-13 10:40:16.298][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-01-13 10:40:16.301][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-01-13 10:40:16.303][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-01-13 10:40:16.305][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-01-13 10:40:16.308][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-01-13 10:40:16.311][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-01-13 10:40:16.313][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-01-13 10:40:16.315][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-01-13 10:40:16.317][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-01-13 10:40:16.320][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-01-13 10:40:16.322][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-01-13 10:40:16.323][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-01-13 10:40:16.325][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-01-13 10:40:16.327][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-01-13 10:40:16.328][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-01-13 10:40:16.331][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-01-13 10:40:16.333][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-01-13 10:40:16.335][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-01-13 10:40:16.337][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-01-13 10:40:16.340][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-01-13 10:40:16.343][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-01-13 10:40:16.346][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-01-13 10:40:16.349][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-01-13 10:40:16.352][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-01-13 10:40:16.355][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-01-13 10:40:16.357][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-01-13 10:40:16.360][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-01-13 10:40:16.363][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-01-13 10:40:16.365][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-01-13 10:40:16.368][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-01-13 10:40:16.369][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-01-13 10:40:16.372][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-01-13 10:40:16.374][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-01-13 10:40:16.377][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-01-13 10:40:16.379][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-01-13 10:40:16.381][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-01-13 10:40:16.383][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-01-13 10:40:16.386][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-01-13 10:40:16.388][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-01-13 10:40:16.390][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-01-13 10:40:16.392][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-01-13 10:40:16.395][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-01-13 10:40:16.397][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-01-13 10:40:16.400][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-01-13 10:40:16.402][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-01-13 10:40:16.405][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-01-13 10:40:16.408][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-01-13 10:40:16.411][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-01-13 10:40:16.413][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-01-13 10:40:16.416][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-01-13 10:40:16.419][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-01-13 10:40:16.421][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-01-13 10:40:16.423][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-01-13 10:40:16.426][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-01-13 10:40:16.429][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-01-13 10:40:16.432][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-01-13 10:40:16.434][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-01-13 10:40:16.436][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-01-13 10:40:16.439][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-01-13 10:40:16.441][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-01-13 10:40:16.451][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-01-13 10:40:16.454][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-01-13 10:40:16.461][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-01-13 10:40:16.462][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.466][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:16.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:16.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:16.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:16.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:16.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:16.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.509][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[2022-01-13 10:40:16.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:16.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:16.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.519][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[2022-01-13 10:40:16.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:16.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:16.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:16.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:16.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:16.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:16.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:16.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:16.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:16.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:16.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:16.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:16.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.581][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[2022-01-13 10:40:16.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:16.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:16.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:16.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:16.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:16.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:16.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:16.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:16.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:16.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:16.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:16.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:16.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:40:16.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:16.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:16.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:16.655][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-01-13 10:40:16.672][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-01-13 10:40:16.676][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-01-13 10:40:16.685][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-01-13 10:40:16.687][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:16.689][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-13 10:40:16.690][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:16.692][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-13 10:40:16.694][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:16.695][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-13 10:40:16.697][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-01-13 10:40:16.699][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-13 10:40:16.701][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:16.702][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-01-13 10:40:16.704][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-13 10:40:16.705][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-01-13 10:40:16.705][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-01-13 10:40:16.705][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-01-13 10:40:16.705][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-01-13 10:40:16.705][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-01-13 10:40:16.705][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-01-13 10:40:16.705][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-01-13 10:40:16.705][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-01-13 10:40:16.705][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-01-13 10:40:16.707][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-01-13 10:40:16.709][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-01-13 10:40:16.709][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-01-13 10:40:16.710][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-13 10:40:16.712][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:40:16.713][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:40:16.715][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-13 10:40:16.717][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:40:16.718][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:40:16.720][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-13 10:40:16.722][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-01-13 10:40:16.722][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-01-13 10:40:16.724][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-13 10:40:16.725][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-13 10:40:16.727][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-01-13 10:40:16.729][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:40:16.737][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-01-13 10:40:16.739][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-01-13 10:40:16.776][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-01-13 10:40:16.778][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-01-13 10:40:16.786][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-01-13 10:40:16.793][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-01-13 10:40:16.800][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-01-13 10:40:16.802][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-01-13 10:40:16.804][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-01-13 10:40:16.806][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-01-13 10:40:16.844][biodb::testThat] 
biodb.INFO [2022-01-13 10:40:16.845][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2022-01-13 10:40:16.847][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:40:16.849][biodb::testThat] 
biodb.TRACE[2022-01-13 10:40:16.855][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2022-01-13 10:40:16.864][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-01-13 10:40:16.866][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-01-13 10:40:16.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:40:16.884][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:16.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:16.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:16.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:16.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:16.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:40:16.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:16.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:16.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:16.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:16.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:16.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:16.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:16.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:16.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-13 10:40:16.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-13 10:40:16.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:16.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:16.965][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-01-13 10:40:16.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-01-13 10:40:16.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:16.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:16.972][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-01-13 10:40:16.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-01-13 10:40:16.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:16.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:16.979][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:16.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:16.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:16.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.031][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:17.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:17.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.043][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:17.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:17.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.050][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:17.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:17.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.063][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-13 10:40:17.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:17.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.068][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-13 10:40:17.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:17.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.078][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:40:17.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:40:17.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.087][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:40:17.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:40:17.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.100][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:17.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:17.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.105][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:17.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:17.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.131][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-13 10:40:17.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:17.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.138][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-01-13 10:40:17.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:17.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:17.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:17.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.154][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:17.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:17.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.161][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-13 10:40:17.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:17.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.204][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:17.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:17.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.212][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:17.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:17.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.296][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:17.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:17.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.303][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:17.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:17.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.311][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:17.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:17.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.326][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:17.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:17.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.335][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:17.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:17.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.352][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:17.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:17.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-13 10:40:17.413][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2022-01-13 10:40:17.424][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-13 10:40:17.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-13 10:40:17.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.432][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-13 10:40:17.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-13 10:40:17.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.439][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-01-13 10:40:17.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-01-13 10:40:17.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.445][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-01-13 10:40:17.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-01-13 10:40:17.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.534][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:17.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:17.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.588][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:17.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:17.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.596][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:17.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:17.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.604][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:17.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:17.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.643][ef$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.645][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.647][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.649][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.668][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:17.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:17.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.674][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:17.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:17.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.682][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:17.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:17.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.688][ef$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:17.690][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:17.692][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.694][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:17.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:17.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.713][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:17.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:17.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.720][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:17.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:17.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.727][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:17.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:17.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.734][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:17.736][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:17.737][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.739][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.741][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:17.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:17.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.754][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:40:17.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:40:17.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.760][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:40:17.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:40:17.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.767][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:40:17.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:40:17.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.773][ef$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:40:17.775][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:40:17.776][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.777][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.779][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:40:17.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:40:17.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:17.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:17.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:17.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:17.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:17.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:17.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.816][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:17.818][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:17.820][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.821][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:17.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:17.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.837][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:17.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:17.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.843][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:17.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:17.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.852][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:17.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:17.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.859][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:17.861][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:17.863][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.864][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.865][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:17.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:17.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.881][ef$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:17.883][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:17.884][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.885][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.891][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:17.893][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:17.895][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.896][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.902][ef$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:40:17.905][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:40:17.907][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.909][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.921][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:17.923][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:17.925][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.926][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.932][ef$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:17.935][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:17.936][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.938][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:17.944][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:17.946][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:17.949][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:17.951][ef$get] fields variable is a list.
biodb.INFO [2022-01-13 10:40:17.957][biodb::testThat] 
biodb.INFO [2022-01-13 10:40:17.959][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2022-01-13 10:40:17.960][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:40:17.961][biodb::testThat] 
biodb.DEBUG[2022-01-13 10:40:17.985][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2022-01-13 10:40:18.000][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2022-01-13 10:40:18.006][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.INFO [2022-01-13 10:40:18.008][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2022-01-13 10:40:18.010][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-01-13 10:40:18.013][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-01-13 10:40:18.015][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-01-13 10:40:18.017][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-01-13 10:40:18.019][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-01-13 10:40:18.021][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-01-13 10:40:18.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:40:18.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:18.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:18.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:18.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:18.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:18.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:18.042][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2022-01-13 10:40:18.076][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:40:18.078][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:40:18.080][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2022-01-13 10:40:19.451][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.DEBUG[2022-01-13 10:40:20.163][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:40:20.180][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.content"
biodb.TRACE[2022-01-13 10:40:20.225][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.request"
biodb.TRACE[2022-01-13 10:40:20.248][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv"
biodb.DEBUG[2022-01-13 10:40:20.258][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-01-13 10:40:20.329][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-01-13 10:40:20.331][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-01-13 10:40:20.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:40:20.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:20.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:20.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:20.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:20.345][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:20.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:40:20.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:20.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:20.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:20.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:20.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-13 10:40:20.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-13 10:40:20.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.382][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-01-13 10:40:20.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-01-13 10:40:20.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.387][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-01-13 10:40:20.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-01-13 10:40:20.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.437][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:20.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:20.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.445][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:20.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:20.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.459][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:20.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:20.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.467][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:20.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:20.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.482][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-13 10:40:20.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:20.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.490][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-13 10:40:20.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:20.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.506][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:40:20.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:40:20.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.513][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:40:20.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:40:20.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.527][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:20.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:20.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.532][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:20.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:20.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.541][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-13 10:40:20.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:20.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.548][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-01-13 10:40:20.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:20.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.556][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:20.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:20.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.563][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:20.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:20.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.570][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-13 10:40:20.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:20.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.585][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:20.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:20.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:20.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:20.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:20.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:20.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.604][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:20.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:20.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:20.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:20.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.627][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:20.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:20.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.633][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:20.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:20.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:20.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:20.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.647][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:20.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:20.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:20.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:20.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:20.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:20.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:20.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:20.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:20.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:20.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:20.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:20.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:20.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:20.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-13 10:40:20.702][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2022-01-13 10:40:20.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-01-13 10:40:20.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-01-13 10:40:20.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-01-13 10:40:20.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-01-13 10:40:20.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-01-13 10:40:20.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-01-13 10:40:20.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-01-13 10:40:20.734][biodb::testThat] 
biodb.INFO [2022-01-13 10:40:20.735][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2022-01-13 10:40:20.737][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:40:20.739][biodb::testThat] 
biodb.TRACE[2022-01-13 10:40:20.744][ef$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:20.746][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:20.748][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.750][ef$get] fields variable is a list.
biodb.DEBUG[2022-01-13 10:40:20.759][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2022-01-13 10:40:20.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:20.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:20.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.802][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:20.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:20.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:20.809][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:20.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:20.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:20.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-13 10:40:20.819][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-01-13 10:40:20.906][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-01-13 10:40:20.940][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:40:20.941][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:40:20.965][private$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[2022-01-13 10:40:21.636][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[2022-01-13 10:40:22.339][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:40:22.353][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.INFO [2022-01-13 10:40:22.380][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2022-01-13 10:40:22.383][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2022-01-13 10:40:22.394][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2022-01-13 10:40:22.403][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:22.404][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:22.405][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:22.406][ef$get] fields variable is a list.
biodb.INFO [2022-01-13 10:40:22.408][biodb::testThat] 
biodb.INFO [2022-01-13 10:40:22.410][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2022-01-13 10:40:22.411][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:40:22.412][biodb::testThat] 
biodb.TRACE[2022-01-13 10:40:22.427][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:22.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:22.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:22.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:22.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:22.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:22.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:22.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:22.441][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:22.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:22.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:22.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-13 10:40:22.616][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-01-13 10:40:22.621][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:40:22.623][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:40:22.626][private$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[2022-01-13 10:40:23.288][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[2022-01-13 10:40:23.952][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:40:23.960][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2022-01-13 10:40:23.975][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.INFO [2022-01-13 10:40:23.991][biodb::testThat] 
biodb.INFO [2022-01-13 10:40:23.993][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2022-01-13 10:40:23.995][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:40:23.996][biodb::testThat] 
biodb.TRACE[2022-01-13 10:40:24.030][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-13 10:40:24.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-13 10:40:24.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:24.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:24.035][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-13 10:40:24.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-13 10:40:24.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:24.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:24.040][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-01-13 10:40:24.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-01-13 10:40:24.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:24.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:24.044][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-01-13 10:40:24.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-01-13 10:40:24.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:24.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:24.128][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-13 10:40:24.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-13 10:40:24.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:24.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:24.134][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-13 10:40:24.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-13 10:40:24.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:24.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:24.140][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-01-13 10:40:24.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-01-13 10:40:24.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:24.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:24.145][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-01-13 10:40:24.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-01-13 10:40:24.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:24.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-01-13 10:40:24.154][biodb::testThat] 
biodb.INFO [2022-01-13 10:40:24.155][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2022-01-13 10:40:24.156][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:40:24.157][biodb::testThat] 
biodb.INFO [2022-01-13 10:40:24.162][biodb::testThat] 
biodb.INFO [2022-01-13 10:40:24.163][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2022-01-13 10:40:24.164][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:40:24.165][biodb::testThat] 
biodb.INFO [2022-01-13 10:40:24.170][biodb::testThat] 
biodb.INFO [2022-01-13 10:40:24.172][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2022-01-13 10:40:24.173][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:40:24.174][biodb::testThat] 
biodb.DEBUG[2022-01-13 10:40:24.177][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2022-01-13 10:40:24.940][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2022-01-13 10:40:25.368][biodb::testThat] 
biodb.INFO [2022-01-13 10:40:25.370][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2022-01-13 10:40:25.371][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:40:25.372][biodb::testThat] 
biodb.INFO [2022-01-13 10:40:25.378][biodb::testThat] 
biodb.INFO [2022-01-13 10:40:25.380][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2022-01-13 10:40:25.381][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:40:25.383][biodb::testThat] 
biodb.TRACE[2022-01-13 10:40:25.394][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:25.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:25.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:25.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:25.401][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:25.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:25.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:25.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:25.407][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:25.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:25.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:25.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-13 10:40:25.545][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[2022-01-13 10:40:25.720][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-01-13 10:40:25.750][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-01-13 10:40:25.752][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-01-13 10:40:25.755][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2022-01-13 10:40:25.785][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[2022-01-13 10:40:25.789][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-01-13 10:40:25.791][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-01-13 10:40:25.792][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-01-13 10:40:25.794][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2022-01-13 10:40:25.806][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-01-13 10:40:25.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-01-13 10:40:25.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:25.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:25.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-01-13 10:40:25.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-01-13 10:40:25.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:25.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:25.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:25.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:25.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:25.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:25.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:25.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:25.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:25.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:25.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:25.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:25.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:25.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:25.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:25.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:25.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:25.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:25.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:25.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:25.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:25.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-13 10:40:25.917][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[2022-01-13 10:40:25.922][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:40:25.923][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:40:25.925][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2022-01-13 10:40:30.312][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2022-01-13 10:40:36.651][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:40:36.658][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2022-01-13 10:40:36.743][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2022-01-13 10:40:37.336][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2022-01-13 10:40:37.342][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:40:37.343][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:40:37.346][private$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[2022-01-13 10:40:37.999][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[2022-01-13 10:40:38.663][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:40:38.670][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2022-01-13 10:40:38.682][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2022-01-13 10:40:38.737][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[2022-01-13 10:40:38.741][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:40:38.742][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:40:38.744][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2022-01-13 10:40:39.368][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2022-01-13 10:40:40.077][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:40:40.086][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2022-01-13 10:40:40.101][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2022-01-13 10:40:40.123][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-01-13 10:40:40.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-01-13 10:40:40.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:40.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-01-13 10:40:40.135][biodb::testThat] 
biodb.INFO [2022-01-13 10:40:40.137][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2022-01-13 10:40:40.138][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:40:40.140][biodb::testThat] 
biodb.TRACE[2022-01-13 10:40:40.146][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-01-13 10:40:40.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-01-13 10:40:40.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:40.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:40.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-01-13 10:40:40.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-01-13 10:40:40.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:40.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:40.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:40.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:40.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:40.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:40.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:40.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:40.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:40.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:40.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:40.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:40.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:40.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:40.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:40.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:40.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:40.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-13 10:40:40.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:40:40.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:40.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:40.202][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:40.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:40.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:40.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:40.335][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2022-01-13 10:40:40.339][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:40:40.341][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:40:40.343][private$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[2022-01-13 10:40:44.775][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[2022-01-13 10:40:50.828][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:40:50.846][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2022-01-13 10:40:50.950][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2022-01-13 10:40:51.414][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2022-01-13 10:40:51.502][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-01-13 10:40:51.505][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2022-01-13 10:40:51.507][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2022-01-13 10:40:51.509][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-01-13 10:40:51.512][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-01-13 10:40:51.514][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-01-13 10:40:51.516][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-01-13 10:40:51.518][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-01-13 10:40:51.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:40:51.563][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:51.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:51.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:51.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:51.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:51.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:51.576][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2022-01-13 10:40:51.582][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:40:51.584][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:40:51.587][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2022-01-13 10:40:52.308][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2022-01-13 10:40:53.006][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:40:53.021][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2022-01-13 10:40:53.048][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2022-01-13 10:40:53.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:40:53.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:53.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:53.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:53.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:53.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:53.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:53.186][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2022-01-13 10:40:53.190][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:40:53.192][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:40:53.195][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2022-01-13 10:40:53.863][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2022-01-13 10:40:54.591][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:40:54.608][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2022-01-13 10:40:54.634][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2022-01-13 10:40:54.660][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2022-01-13 10:40:54.668][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-01-13 10:40:54.686][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-01-13 10:40:54.688][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-01-13 10:40:54.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:40:54.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:54.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:54.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:54.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:54.699][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:54.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:40:54.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:54.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:54.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:54.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:54.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-13 10:40:54.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-13 10:40:54.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-13 10:40:54.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-13 10:40:54.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.749][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-01-13 10:40:54.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-01-13 10:40:54.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.756][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-01-13 10:40:54.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-01-13 10:40:54.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.762][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:54.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:54.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.767][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:54.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:54.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.782][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:54.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:54.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.789][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:54.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:54.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.823][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-13 10:40:54.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:54.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.829][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-13 10:40:54.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:54.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.843][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:40:54.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:40:54.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.849][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:40:54.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:40:54.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.863][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:54.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:54.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:54.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:54.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.885][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-13 10:40:54.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:54.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.892][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-01-13 10:40:54.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:54.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.901][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:54.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:54.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.909][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:54.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:54.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.917][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-13 10:40:54.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:54.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.931][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:54.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:54.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.940][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:54.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:54.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:54.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:54.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.955][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:54.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:54.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:54.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:54.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:54.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:54.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:54.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:54.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:54.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:54.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-13 10:40:54.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:40:54.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:54.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:54.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:54.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:54.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:55.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:40:55.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:55.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:55.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:55.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:55.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-13 10:40:55.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-13 10:40:55.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.035][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-01-13 10:40:55.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-01-13 10:40:55.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.042][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-01-13 10:40:55.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-01-13 10:40:55.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.047][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:55.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:55.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.056][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:55.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:40:55.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.069][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:55.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:55.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.087][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:55.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:40:55.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.097][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-13 10:40:55.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:55.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.102][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-13 10:40:55.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:55.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.115][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:40:55.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:40:55.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.122][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:40:55.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:40:55.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:55.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:55.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.139][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:55.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:55.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.150][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-13 10:40:55.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:55.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.157][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-01-13 10:40:55.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:55.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.163][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:55.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:55.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.170][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:40:55.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:55.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.178][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-13 10:40:55.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:40:55.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.191][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.199][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:55.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:55.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.211][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:55.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:55.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:55.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:55.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:55.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:55.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:55.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:55.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:55.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:55.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:55.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:55.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:55.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:55.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:55.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:55.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:40:55.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:40:55.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-13 10:40:55.274][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2022-01-13 10:40:55.286][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-01-13 10:40:55.288][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:40:55.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:55.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:55.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:55.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:55.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:55.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:40:55.298][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.321][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.328][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:40:55.330][private$selectFields] 
biodb.TRACE[2022-01-13 10:40:55.331][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-01-13 10:40:55.333][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-13 10:40:55.335][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:40:55.337][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.339][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.340][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.342][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.343][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.345][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.346][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.348][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.349][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:40:55.351][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:40:55.352][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.353][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.354][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.355][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.356][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-01-13 10:40:55.358][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.365][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.373][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.395][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-01-13 10:40:55.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:40:55.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:55.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:55.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:55.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:55.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:55.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:40:55.408][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.415][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.421][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:40:55.422][private$selectFields] 
biodb.TRACE[2022-01-13 10:40:55.424][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-01-13 10:40:55.427][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-13 10:40:55.428][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:40:55.430][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.432][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.434][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.436][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.437][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.439][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.441][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.443][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.445][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:40:55.446][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:40:55.447][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.449][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.450][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.452][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.453][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-01-13 10:40:55.455][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.461][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.467][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.475][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-01-13 10:40:55.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:40:55.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:55.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:55.483][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:55.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:55.486][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:55.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:40:55.490][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.497][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.504][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:40:55.506][private$selectFields] 
biodb.TRACE[2022-01-13 10:40:55.508][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-01-13 10:40:55.510][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-13 10:40:55.511][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:40:55.513][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.514][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.515][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.516][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.517][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.519][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.520][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.521][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.522][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:40:55.523][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:40:55.524][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.526][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.528][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.530][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.532][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-01-13 10:40:55.534][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.541][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.548][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:40:55.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.557][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-01-13 10:40:55.572][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-01-13 10:40:55.573][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-01-13 10:40:55.585][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-01-13 10:40:55.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-01-13 10:40:55.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-01-13 10:40:55.593][biodb::testThat] 
biodb.INFO [2022-01-13 10:40:55.594][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2022-01-13 10:40:55.596][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:40:55.598][biodb::testThat] 
biodb.TRACE[2022-01-13 10:40:55.602][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-01-13 10:40:55.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-01-13 10:40:55.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-01-13 10:40:55.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-01-13 10:40:55.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:55.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:55.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:55.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:55.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:55.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:55.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:40:55.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:55.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:40:55.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:40:55.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-13 10:40:55.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:40:55.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:40:55.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:40:55.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:40:55.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:40:55.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:40:55.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:40:55.879][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2022-01-13 10:40:55.885][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:40:55.887][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:40:55.889][private$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[2022-01-13 10:41:00.286][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[2022-01-13 10:41:06.239][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:41:06.257][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2022-01-13 10:41:06.354][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2022-01-13 10:41:06.850][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-01-13 10:41:06.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:41:06.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:06.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:06.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:06.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:06.912][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:06.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:41:06.929][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:06.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:06.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:06.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:06.934][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:06.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:06.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:06.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:06.985][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:06.986][private$selectFields] 
biodb.TRACE[2022-01-13 10:41:06.987][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-01-13 10:41:06.988][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-13 10:41:06.990][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:06.991][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:06.992][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:06.993][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:06.994][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:06.996][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:06.997][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:06.998][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:06.999][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.000][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:07.014][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:07.015][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.016][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.018][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.019][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.020][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-01-13 10:41:07.022][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.027][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.032][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.041][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-01-13 10:41:07.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:41:07.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:07.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:07.051][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:07.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:07.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:07.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:41:07.058][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.064][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.072][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:07.074][private$selectFields] 
biodb.TRACE[2022-01-13 10:41:07.075][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-01-13 10:41:07.077][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-13 10:41:07.078][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:07.079][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.081][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.083][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.084][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.086][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.088][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.090][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.091][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.092][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:07.093][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:07.096][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.098][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.100][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.101][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.103][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-01-13 10:41:07.105][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.113][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.119][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.128][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-01-13 10:41:07.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:41:07.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:07.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:07.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:07.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:07.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:07.143][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[2022-01-13 10:41:07.145][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.151][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.156][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:07.157][private$selectFields] 
biodb.TRACE[2022-01-13 10:41:07.158][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-01-13 10:41:07.160][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-13 10:41:07.161][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:07.163][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.165][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.167][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.169][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.170][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.172][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.173][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.174][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.176][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:07.177][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:07.178][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.179][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.181][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.182][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.183][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-01-13 10:41:07.184][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.190][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.215][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:07.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.222][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-01-13 10:41:07.224][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-01-13 10:41:07.226][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-01-13 10:41:07.236][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-01-13 10:41:07.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-01-13 10:41:07.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-01-13 10:41:07.244][biodb::testThat] 
biodb.INFO [2022-01-13 10:41:07.245][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2022-01-13 10:41:07.246][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:41:07.247][biodb::testThat] 
biodb.TRACE[2022-01-13 10:41:07.250][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-01-13 10:41:07.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-01-13 10:41:07.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-01-13 10:41:07.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-01-13 10:41:07.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:41:07.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:41:07.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:41:07.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:41:07.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:41:07.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:41:07.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:07.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:41:07.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:41:07.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:07.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-13 10:41:07.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:41:07.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:07.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:07.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:07.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:07.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:07.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:07.407][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[2022-01-13 10:41:07.412][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-01-13 10:41:07.414][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2022-01-13 10:41:07.417][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-01-13 10:41:07.465][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2022-01-13 10:41:08.536][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-01-13 10:41:08.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:41:08.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:08.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:08.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:08.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:08.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:08.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:41:08.592][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.600][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.607][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:08.608][private$selectFields] 
biodb.TRACE[2022-01-13 10:41:08.609][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-01-13 10:41:08.611][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-13 10:41:08.613][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:08.615][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.617][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.618][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.619][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.621][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.622][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.623][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.624][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.625][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:08.627][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:08.628][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.629][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.630][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.631][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.632][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-01-13 10:41:08.634][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.638][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.644][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.649][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-01-13 10:41:08.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:41:08.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:08.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:08.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:08.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:08.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:08.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:41:08.659][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.663][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.671][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:08.673][private$selectFields] 
biodb.TRACE[2022-01-13 10:41:08.674][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-01-13 10:41:08.675][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-13 10:41:08.676][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:08.678][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.679][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.681][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.683][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.685][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.687][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.689][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.690][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.691][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:08.692][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:08.693][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.695][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.697][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.698][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.700][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-01-13 10:41:08.702][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.707][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.712][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.717][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-01-13 10:41:08.718][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:41:08.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:08.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:08.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:08.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:08.725][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:08.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:41:08.728][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.737][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.745][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:08.746][private$selectFields] 
biodb.TRACE[2022-01-13 10:41:08.748][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-01-13 10:41:08.750][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-13 10:41:08.751][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:08.752][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.753][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.754][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.756][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.758][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.761][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.763][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.764][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.766][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:08.768][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:41:08.770][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.772][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.774][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.776][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.778][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-01-13 10:41:08.780][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.787][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.795][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:08.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:08.803][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-01-13 10:41:08.804][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-01-13 10:41:08.806][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-01-13 10:41:08.838][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-01-13 10:41:08.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-01-13 10:41:08.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:08.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-01-13 10:41:08.845][biodb::testThat] 
biodb.INFO [2022-01-13 10:41:08.846][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2022-01-13 10:41:08.848][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:41:08.849][biodb::testThat] 
biodb.DEBUG[2022-01-13 10:41:08.852][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2022-01-13 10:41:08.853][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2022-01-13 10:41:08.855][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2022-01-13 10:41:08.857][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-01-13 10:41:08.858][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-01-13 10:41:08.860][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-01-13 10:41:08.862][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-01-13 10:41:08.864][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-01-13 10:41:08.866][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-01-13 10:41:08.871][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:41:08.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:08.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:08.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:08.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:08.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:08.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:08.880][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2022-01-13 10:41:08.885][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:08.887][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:08.889][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-13 10:41:09.496][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:09.498][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:09.500][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[2022-01-13 10:41:09.503][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-13 10:41:10.387][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-01-13 10:41:10.389][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:10.391][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:10.394][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-13 10:41:11.022][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:11.023][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:11.025][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-13 10:41:11.028][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-13 10:41:11.920][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-01-13 10:41:11.921][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:11.922][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:11.924][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-13 10:41:12.618][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:12.620][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:12.622][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[2022-01-13 10:41:12.648][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-13 10:41:13.544][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-01-13 10:41:13.545][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:13.546][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:13.549][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-13 10:41:14.228][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:14.230][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:14.231][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[2022-01-13 10:41:14.233][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-13 10:41:15.158][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-01-13 10:41:15.160][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:15.162][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:15.164][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-13 10:41:15.801][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:15.803][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:15.805][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[2022-01-13 10:41:15.807][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-13 10:41:16.574][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-01-13 10:41:16.575][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:16.577][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:16.579][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-13 10:41:17.234][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:17.236][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:17.238][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[2022-01-13 10:41:17.240][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-13 10:41:18.274][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-01-13 10:41:18.276][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:18.278][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:18.280][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-13 10:41:18.908][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:18.910][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:18.912][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[2022-01-13 10:41:18.914][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-13 10:41:19.727][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-01-13 10:41:19.729][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:19.730][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:19.733][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-13 10:41:20.382][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:20.384][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:20.386][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[2022-01-13 10:41:20.388][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-13 10:41:21.258][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-01-13 10:41:21.260][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:21.261][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:21.263][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-13 10:41:21.949][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:21.951][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:21.953][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[2022-01-13 10:41:21.955][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-13 10:41:22.927][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-01-13 10:41:22.929][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:22.930][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:22.932][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-13 10:41:23.975][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:23.976][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:23.978][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[2022-01-13 10:41:23.980][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-13 10:41:24.706][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2022-01-13 10:41:24.724][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2022-01-13 10:41:24.733][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-01-13 10:41:24.754][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-01-13 10:41:24.756][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-01-13 10:41:24.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:41:24.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:24.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:24.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:24.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:24.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:24.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:41:24.774][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:24.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:24.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:24.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:24.782][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:24.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:24.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:24.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:24.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:24.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:24.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:24.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:24.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:24.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:24.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:24.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:24.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:24.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:24.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:24.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:24.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:24.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:24.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:24.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:24.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:24.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:24.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:24.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:24.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:24.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:24.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:24.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-13 10:41:24.827][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2022-01-13 10:41:24.829][self$createEntryFromContent] Found %d entry/ies without an accession number. Set it/them to NULL.1
biodb.INFO [2022-01-13 10:41:24.835][biodb::testThat] 
biodb.INFO [2022-01-13 10:41:24.837][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2022-01-13 10:41:24.839][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:41:24.841][biodb::testThat] 
biodb.DEBUG[2022-01-13 10:41:24.856][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2022-01-13 10:41:24.858][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2022-01-13 10:41:24.860][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-01-13 10:41:24.864][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2022-01-13 10:41:24.866][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2022-01-13 10:41:24.869][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-01-13 10:41:24.871][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-01-13 10:41:24.873][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-01-13 10:41:24.875][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-01-13 10:41:24.877][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-01-13 10:41:24.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:41:24.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:24.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:24.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:24.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:24.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:24.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:24.910][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2022-01-13 10:41:24.914][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:24.916][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:24.919][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-13 10:41:25.541][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:25.542][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:25.543][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-13 10:41:25.545][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-13 10:41:26.449][private$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[2022-01-13 10:41:26.451][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:26.453][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:26.456][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-13 10:41:27.051][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:27.052][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:27.053][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-13 10:41:27.055][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-13 10:41:27.917][private$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[2022-01-13 10:41:27.918][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:27.920][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:27.921][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-13 10:41:28.568][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:28.570][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:28.572][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-13 10:41:28.574][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-13 10:41:29.353][private$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[2022-01-13 10:41:29.355][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:29.357][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:29.375][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-13 10:41:30.016][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:30.018][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:30.020][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-13 10:41:30.022][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-13 10:41:30.745][private$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[2022-01-13 10:41:30.746][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:30.748][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:30.750][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-13 10:41:31.470][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:31.472][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:31.474][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-13 10:41:31.476][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-13 10:41:32.239][private$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[2022-01-13 10:41:32.240][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:32.241][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:32.244][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-13 10:41:32.896][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:32.897][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:32.899][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-13 10:41:32.901][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-13 10:41:33.738][private$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[2022-01-13 10:41:33.740][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:33.742][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:33.745][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-13 10:41:34.440][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:34.442][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:34.444][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-13 10:41:34.446][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-13 10:41:35.234][private$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[2022-01-13 10:41:35.235][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:35.237][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:35.240][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-13 10:41:35.899][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:35.901][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:35.903][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-13 10:41:35.905][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-13 10:41:36.765][private$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[2022-01-13 10:41:36.767][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:36.768][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:36.770][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-13 10:41:37.423][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:37.425][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:37.426][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-13 10:41:37.428][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-13 10:41:38.346][private$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[2022-01-13 10:41:38.348][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:38.350][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:38.353][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-13 10:41:39.058][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-13 10:41:39.060][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-13 10:41:39.062][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-13 10:41:39.064][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-13 10:41:39.954][private$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[2022-01-13 10:41:39.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:41:39.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:39.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:39.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:39.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:39.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:39.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:39.968][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2022-01-13 10:41:39.973][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:39.976][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:39.978][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2022-01-13 10:41:40.640][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2022-01-13 10:41:41.329][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:41:41.343][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2022-01-13 10:41:41.365][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2022-01-13 10:41:41.391][private$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[2022-01-13 10:41:41.422][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-01-13 10:41:41.438][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-01-13 10:41:41.440][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-01-13 10:41:41.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:41:41.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:41.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:41.446][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:41.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:41.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:41.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:41:41.451][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:41.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:41.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.456][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:41.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:41.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:41.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:41.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-13 10:41:41.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:41:41.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:41.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:41.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:41.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:41.477][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:41.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:41:41.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:41.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:41.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:41.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:41.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-13 10:41:41.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-13 10:41:41.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-13 10:41:41.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-13 10:41:41.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.528][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-01-13 10:41:41.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-01-13 10:41:41.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.535][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-01-13 10:41:41.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-01-13 10:41:41.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.547][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-01-13 10:41:41.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-01-13 10:41:41.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.553][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-01-13 10:41:41.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-01-13 10:41:41.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.562][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:41:41.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:41:41.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.568][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:41:41.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:41:41.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.580][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:41:41.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:41:41.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.590][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:41:41.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:41:41.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.607][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-13 10:41:41.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:41:41.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.616][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-13 10:41:41.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:41:41.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.628][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:41:41.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:41:41.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.637][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:41:41.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:41:41.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.653][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:41:41.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:41:41.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.659][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:41:41.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:41:41.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.669][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-13 10:41:41.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:41:41.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.685][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-01-13 10:41:41.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:41:41.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:41:41.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:41:41.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:41:41.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:41:41.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.703][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-13 10:41:41.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:41:41.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.718][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:41:41.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:41:41.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.726][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:41:41.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:41:41.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.735][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:41:41.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:41:41.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.740][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:41:41.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:41:41.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.748][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:41:41.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:41:41.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.764][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:41.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:41.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.772][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:41.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:41.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:41.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:41.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.786][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:41.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:41:41.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:41.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:41.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:41.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:41.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:41.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:41.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:41.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:41.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:41.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:41.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:41.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:41.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:41.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:41.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:41.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:41.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:41.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:41.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:41.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:41.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:41:41.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:41:41.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:41:41.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:41:41.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-13 10:41:41.896][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2022-01-13 10:41:41.898][self$createEntryFromContent] Found %d entry/ies without an accession number. Set it/them to NULL.1
biodb.DEBUG[2022-01-13 10:41:41.900][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2022-01-13 10:41:41.914][biodb::testThat] 
biodb.INFO [2022-01-13 10:41:41.916][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2022-01-13 10:41:41.918][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:41:41.919][biodb::testThat] 
biodb.INFO [2022-01-13 10:41:41.955][biodb::testThat] 
biodb.INFO [2022-01-13 10:41:41.957][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2022-01-13 10:41:41.959][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:41:41.961][biodb::testThat] 
biodb.INFO [2022-01-13 10:41:41.969][biodb::testThat] 
biodb.INFO [2022-01-13 10:41:41.971][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2022-01-13 10:41:41.972][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:41:41.974][biodb::testThat] 
biodb.DEBUG[2022-01-13 10:41:42.022][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2022-01-13 10:41:42.025][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:42.026][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:42.028][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2022-01-13 10:41:46.473][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2022-01-13 10:41:52.619][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:41:52.634][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2022-01-13 10:41:52.726][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.INFO [2022-01-13 10:41:53.260][biodb::testThat] 
biodb.INFO [2022-01-13 10:41:53.262][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2022-01-13 10:41:53.264][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:41:53.266][biodb::testThat] 
biodb.ERROR[2022-01-13 10:41:53.283][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2022-01-13 10:41:53.305][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2022-01-13 10:41:53.318][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-01-13 10:41:53.320][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-01-13 10:41:53.322][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-01-13 10:41:53.324][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-01-13 10:41:53.325][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:53.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:53.329][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:53.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:53.331][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.332][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.INFO [2022-01-13 10:41:53.337][biodb::testContext] 
biodb.INFO [2022-01-13 10:41:53.339][biodb::testContext] ********************************************************************************
biodb.INFO [2022-01-13 10:41:53.340][biodb::testContext] Test context - Web services tests
biodb.INFO [2022-01-13 10:41:53.341][biodb::testContext] ********************************************************************************
biodb.INFO [2022-01-13 10:41:53.342][biodb::testContext] 
biodb.INFO [2022-01-13 10:41:53.349][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-01-13 10:41:53.351][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-01-13 10:41:53.356][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-01-13 10:41:53.357][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-01-13 10:41:53.358][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-01-13 10:41:53.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.362][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-01-13 10:41:53.364][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-01-13 10:41:53.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.368][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-01-13 10:41:53.369][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-01-13 10:41:53.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.373][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-01-13 10:41:53.374][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-01-13 10:41:53.376][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-01-13 10:41:53.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.380][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-01-13 10:41:53.382][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-01-13 10:41:53.384][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-01-13 10:41:53.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.388][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-01-13 10:41:53.390][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-01-13 10:41:53.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.396][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-01-13 10:41:53.398][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-01-13 10:41:53.400][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-01-13 10:41:53.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.408][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-01-13 10:41:53.410][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-01-13 10:41:53.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.417][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-01-13 10:41:53.419][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-01-13 10:41:53.421][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-01-13 10:41:53.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.428][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-01-13 10:41:53.430][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-01-13 10:41:53.432][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-01-13 10:41:53.434][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-01-13 10:41:53.471][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-01-13 10:41:53.473][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-01-13 10:41:53.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.477][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[2022-01-13 10:41:53.479][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-01-13 10:41:53.481][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-01-13 10:41:53.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.487][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-01-13 10:41:53.489][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-01-13 10:41:53.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.496][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-01-13 10:41:53.498][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-01-13 10:41:53.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.505][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-01-13 10:41:53.507][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-01-13 10:41:53.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.514][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-01-13 10:41:53.516][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-01-13 10:41:53.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.522][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-01-13 10:41:53.523][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-01-13 10:41:53.535][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-01-13 10:41:53.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.540][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[2022-01-13 10:41:53.542][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-01-13 10:41:53.544][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-01-13 10:41:53.545][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-01-13 10:41:53.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.552][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-01-13 10:41:53.555][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-01-13 10:41:53.557][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-01-13 10:41:53.559][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:53.560][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-13 10:41:53.562][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:53.563][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-13 10:41:53.565][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-13 10:41:53.567][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-13 10:41:53.569][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-01-13 10:41:53.571][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-13 10:41:53.573][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:53.574][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-01-13 10:41:53.575][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-13 10:41:53.576][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:41:53.578][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:53.580][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-01-13 10:41:53.580][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-01-13 10:41:53.580][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-01-13 10:41:53.580][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-01-13 10:41:53.580][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-01-13 10:41:53.582][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-13 10:41:53.584][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:41:53.586][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:41:53.587][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-13 10:41:53.589][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:41:53.590][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:41:53.591][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-13 10:41:53.592][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:41:53.594][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-13 10:41:53.595][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-13 10:41:53.596][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-13 10:41:53.598][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:41:53.600][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-01-13 10:41:53.604][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-01-13 10:41:53.606][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-01-13 10:41:53.608][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:53.609][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-13 10:41:53.611][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:53.612][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-13 10:41:53.613][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-13 10:41:53.615][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-13 10:41:53.616][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-01-13 10:41:53.617][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-13 10:41:53.619][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:53.621][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-01-13 10:41:53.623][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-13 10:41:53.625][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:41:53.627][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:53.629][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-01-13 10:41:53.629][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-01-13 10:41:53.629][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-01-13 10:41:53.629][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-01-13 10:41:53.629][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-01-13 10:41:53.631][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-13 10:41:53.633][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:41:53.635][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:41:53.637][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-13 10:41:53.638][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:41:53.639][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:41:53.640][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-13 10:41:53.642][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:41:53.644][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-13 10:41:53.645][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-13 10:41:53.647][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-13 10:41:53.649][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:41:53.651][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-01-13 10:41:53.653][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:53.654][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-01-13 10:41:53.655][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:53.657][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-13 10:41:53.659][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:53.662][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-13 10:41:53.664][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-13 10:41:53.666][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-13 10:41:53.668][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-01-13 10:41:53.671][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-13 10:41:53.673][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-01-13 10:41:53.675][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-01-13 10:41:53.676][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-13 10:41:53.677][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:41:53.679][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:53.681][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:41:53.683][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-13 10:41:53.685][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:41:53.687][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:41:53.689][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-13 10:41:53.691][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:41:53.692][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:41:53.694][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-13 10:41:53.696][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:41:53.699][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-13 10:41:53.700][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-13 10:41:53.702][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-13 10:41:53.704][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:41:53.707][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-01-13 10:41:53.709][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:53.711][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-01-13 10:41:53.712][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:53.714][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-13 10:41:53.716][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:53.718][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-13 10:41:53.720][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-13 10:41:53.723][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-13 10:41:53.725][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-01-13 10:41:53.727][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-13 10:41:53.729][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-01-13 10:41:53.751][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-01-13 10:41:53.753][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-13 10:41:53.755][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:41:53.757][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:53.759][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:41:53.760][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-13 10:41:53.761][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:41:53.762][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:41:53.763][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-13 10:41:53.764][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:41:53.766][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:41:53.768][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-13 10:41:53.770][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:41:53.772][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-13 10:41:53.773][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-13 10:41:53.775][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-13 10:41:53.776][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:41:53.778][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-01-13 10:41:53.780][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:53.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:53.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:53.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:53.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:53.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:53.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:53.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:53.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.813][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[2022-01-13 10:41:53.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:53.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:53.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:53.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:53.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.830][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[2022-01-13 10:41:53.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:53.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:53.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.839][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[2022-01-13 10:41:53.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:53.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:53.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:53.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:53.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:53.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:53.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:53.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:53.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:53.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:53.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.874][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[2022-01-13 10:41:53.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:53.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:53.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:53.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:53.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.887][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[2022-01-13 10:41:53.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:53.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:53.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:53.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:53.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:53.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.904][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[2022-01-13 10:41:53.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:53.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:53.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:53.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:53.913][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[2022-01-13 10:41:53.915][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-01-13 10:41:53.917][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-01-13 10:41:53.919][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-01-13 10:41:53.921][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-01-13 10:41:53.923][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-01-13 10:41:53.925][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-01-13 10:41:53.927][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-01-13 10:41:53.930][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-01-13 10:41:53.932][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-01-13 10:41:53.936][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-01-13 10:41:53.938][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-01-13 10:41:53.941][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-01-13 10:41:53.944][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-01-13 10:41:53.948][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-01-13 10:41:53.951][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-01-13 10:41:53.954][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-01-13 10:41:53.957][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-01-13 10:41:53.960][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-01-13 10:41:53.963][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-01-13 10:41:53.967][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-01-13 10:41:53.969][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-01-13 10:41:53.973][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-01-13 10:41:53.976][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-01-13 10:41:53.978][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-01-13 10:41:53.980][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-01-13 10:41:53.982][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-01-13 10:41:53.984][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-01-13 10:41:53.985][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-01-13 10:41:53.987][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-01-13 10:41:53.990][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-01-13 10:41:53.993][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-01-13 10:41:54.014][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-01-13 10:41:54.016][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-01-13 10:41:54.019][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-01-13 10:41:54.022][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-01-13 10:41:54.025][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-01-13 10:41:54.028][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-01-13 10:41:54.031][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-01-13 10:41:54.033][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-01-13 10:41:54.036][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-01-13 10:41:54.039][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-01-13 10:41:54.043][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-01-13 10:41:54.046][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-01-13 10:41:54.049][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-01-13 10:41:54.052][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-01-13 10:41:54.054][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-01-13 10:41:54.057][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-01-13 10:41:54.060][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-01-13 10:41:54.062][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-01-13 10:41:54.064][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-01-13 10:41:54.066][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-01-13 10:41:54.068][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-01-13 10:41:54.071][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-01-13 10:41:54.074][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-01-13 10:41:54.077][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-01-13 10:41:54.080][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-01-13 10:41:54.083][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-01-13 10:41:54.086][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-01-13 10:41:54.089][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-01-13 10:41:54.092][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-01-13 10:41:54.096][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-01-13 10:41:54.098][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-01-13 10:41:54.100][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-01-13 10:41:54.102][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-01-13 10:41:54.104][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-01-13 10:41:54.106][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-01-13 10:41:54.109][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-01-13 10:41:54.112][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-01-13 10:41:54.115][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-01-13 10:41:54.118][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-01-13 10:41:54.121][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-01-13 10:41:54.124][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-01-13 10:41:54.127][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-01-13 10:41:54.129][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-01-13 10:41:54.132][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-01-13 10:41:54.135][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-01-13 10:41:54.137][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-01-13 10:41:54.139][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-01-13 10:41:54.140][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-01-13 10:41:54.142][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-01-13 10:41:54.144][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-01-13 10:41:54.147][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-01-13 10:41:54.150][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-01-13 10:41:54.153][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-01-13 10:41:54.156][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-01-13 10:41:54.158][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-01-13 10:41:54.160][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:54.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:54.163][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:54.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:54.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:54.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:54.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:54.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:54.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:54.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:54.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:54.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:54.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:54.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:54.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:54.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:54.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:54.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:54.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:54.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:54.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:54.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:54.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:54.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:54.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:54.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:54.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:54.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:54.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:54.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:54.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:54.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:54.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:54.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:54.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:54.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:54.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:54.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:54.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:54.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:54.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:54.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:54.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:54.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:54.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:54.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:54.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:54.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:54.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:54.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:54.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:54.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:54.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:54.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:54.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:54.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:54.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:54.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:54.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:54.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:54.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:54.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:54.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:54.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:54.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:54.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:54.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:54.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:54.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:54.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:54.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:54.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:54.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:54.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:54.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:54.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:54.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:54.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:54.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:54.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:54.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:54.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:54.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:54.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:54.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:54.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:54.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:54.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:54.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:54.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:54.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:54.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:54.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:54.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:54.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:54.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:54.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:54.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:54.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:54.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:54.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:54.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:54.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:54.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:54.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:54.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:54.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:54.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:54.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:54.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:54.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:54.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:54.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:54.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:54.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:54.352][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[2022-01-13 10:41:54.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:41:54.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:41:54.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:41:54.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:41:54.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:41:54.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:41:54.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:41:54.361][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-01-13 10:41:54.363][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-01-13 10:41:54.366][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-01-13 10:41:54.367][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-01-13 10:41:54.368][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:54.369][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-13 10:41:54.371][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:54.372][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-13 10:41:54.373][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:54.374][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-13 10:41:54.375][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-01-13 10:41:54.377][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-13 10:41:54.378][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:54.379][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-01-13 10:41:54.380][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-13 10:41:54.381][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-01-13 10:41:54.381][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-01-13 10:41:54.381][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-01-13 10:41:54.381][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-01-13 10:41:54.381][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-01-13 10:41:54.381][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-01-13 10:41:54.381][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-01-13 10:41:54.381][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-01-13 10:41:54.381][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-01-13 10:41:54.382][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-01-13 10:41:54.384][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-01-13 10:41:54.384][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-01-13 10:41:54.385][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-13 10:41:54.386][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:41:54.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:41:54.388][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-13 10:41:54.389][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:41:54.391][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:41:54.393][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-13 10:41:54.395][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-01-13 10:41:54.395][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-01-13 10:41:54.397][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-13 10:41:54.398][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-13 10:41:54.400][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-01-13 10:41:54.402][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:41:54.405][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-01-13 10:41:54.407][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-01-13 10:41:54.412][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-01-13 10:41:54.413][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-01-13 10:41:54.414][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-01-13 10:41:54.416][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-01-13 10:41:54.418][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-01-13 10:41:54.419][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-01-13 10:41:54.420][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-01-13 10:41:54.422][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-01-13 10:41:54.424][biodb::testThat] 
biodb.INFO [2022-01-13 10:41:54.426][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2022-01-13 10:41:54.427][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:41:54.429][biodb::testThat] 
biodb.DEBUG[2022-01-13 10:41:54.470][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[2022-01-13 10:41:54.478][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:54.479][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:54.481][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2022-01-13 10:41:55.155][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2022-01-13 10:41:55.844][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:41:55.861][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2022-01-13 10:41:55.885][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2022-01-13 10:41:55.942][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2022-01-13 10:41:55.950][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:55.952][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:55.955][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2022-01-13 10:41:56.664][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[2022-01-13 10:41:57.361][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:41:57.375][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2022-01-13 10:41:57.403][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2022-01-13 10:41:57.418][biodb::testThat] 
biodb.INFO [2022-01-13 10:41:57.420][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2022-01-13 10:41:57.422][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:41:57.423][biodb::testThat] 
biodb.INFO [2022-01-13 10:41:57.441][biodb::testThat] 
biodb.INFO [2022-01-13 10:41:57.443][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2022-01-13 10:41:57.445][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:41:57.447][biodb::testThat] 
biodb.DEBUG[2022-01-13 10:41:57.487][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[2022-01-13 10:41:57.492][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:57.494][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:57.496][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2022-01-13 10:41:58.076][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2022-01-13 10:41:58.639][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:41:58.652][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2022-01-13 10:41:58.680][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2022-01-13 10:41:58.736][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2022-01-13 10:41:58.741][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-01-13 10:41:58.744][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2022-01-13 10:41:58.746][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-01-13 10:41:58.749][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2022-01-13 10:41:58.817][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2022-01-13 10:41:58.822][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:41:58.824][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:41:58.827][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2022-01-13 10:41:59.334][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[2022-01-13 10:41:59.870][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:41:59.887][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2022-01-13 10:41:59.908][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2022-01-13 10:41:59.957][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[2022-01-13 10:42:00.003][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:42:00.004][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:42:00.006][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2022-01-13 10:42:01.357][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2022-01-13 10:42:03.094][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:42:03.110][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2022-01-13 10:42:03.217][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2022-01-13 10:42:03.344][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2022-01-13 10:42:03.350][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:42:03.353][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:42:03.356][private$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[2022-01-13 10:42:04.749][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[2022-01-13 10:42:07.212][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:42:07.228][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2022-01-13 10:42:07.262][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2022-01-13 10:42:07.348][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-01-13 10:42:07.351][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-01-13 10:42:07.353][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-01-13 10:42:07.354][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-01-13 10:42:07.356][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:07.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:07.359][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:07.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:07.362][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.364][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.INFO [2022-01-13 10:42:07.372][biodb::testContext] 
biodb.INFO [2022-01-13 10:42:07.374][biodb::testContext] ********************************************************************************
biodb.INFO [2022-01-13 10:42:07.376][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2022-01-13 10:42:07.378][biodb::testContext] ********************************************************************************
biodb.INFO [2022-01-13 10:42:07.379][biodb::testContext] 
biodb.INFO [2022-01-13 10:42:07.390][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-01-13 10:42:07.393][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-01-13 10:42:07.401][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-01-13 10:42:07.403][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-01-13 10:42:07.406][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-01-13 10:42:07.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.413][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-01-13 10:42:07.415][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-01-13 10:42:07.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.421][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-01-13 10:42:07.423][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-01-13 10:42:07.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.431][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-01-13 10:42:07.433][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-01-13 10:42:07.435][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-01-13 10:42:07.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.443][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-01-13 10:42:07.445][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-01-13 10:42:07.447][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-01-13 10:42:07.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.479][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-01-13 10:42:07.481][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-01-13 10:42:07.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.489][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-01-13 10:42:07.491][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-01-13 10:42:07.493][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-01-13 10:42:07.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.501][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-01-13 10:42:07.503][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-01-13 10:42:07.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.510][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-01-13 10:42:07.512][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-01-13 10:42:07.514][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-01-13 10:42:07.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.521][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-01-13 10:42:07.523][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-01-13 10:42:07.525][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-01-13 10:42:07.528][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-01-13 10:42:07.530][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-01-13 10:42:07.532][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-01-13 10:42:07.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.539][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-01-13 10:42:07.542][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-01-13 10:42:07.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.548][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-01-13 10:42:07.550][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-01-13 10:42:07.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.556][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-01-13 10:42:07.558][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-01-13 10:42:07.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.565][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-01-13 10:42:07.567][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-01-13 10:42:07.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.574][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-01-13 10:42:07.575][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-01-13 10:42:07.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.583][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-01-13 10:42:07.585][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-01-13 10:42:07.597][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-01-13 10:42:07.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.604][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-01-13 10:42:07.606][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-01-13 10:42:07.609][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-01-13 10:42:07.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.618][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-01-13 10:42:07.622][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-01-13 10:42:07.624][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-01-13 10:42:07.626][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:07.629][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-13 10:42:07.631][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:07.633][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-13 10:42:07.635][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-13 10:42:07.639][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-13 10:42:07.641][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-01-13 10:42:07.644][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-13 10:42:07.646][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:07.653][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-01-13 10:42:07.655][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-13 10:42:07.657][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:42:07.659][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:07.661][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-01-13 10:42:07.661][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-01-13 10:42:07.661][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-01-13 10:42:07.661][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-01-13 10:42:07.661][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-01-13 10:42:07.663][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-13 10:42:07.665][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:42:07.667][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:42:07.669][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-13 10:42:07.671][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:42:07.673][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:42:07.675][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-13 10:42:07.677][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:42:07.680][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-13 10:42:07.682][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-13 10:42:07.684][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-13 10:42:07.686][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:42:07.689][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-01-13 10:42:07.693][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-01-13 10:42:07.695][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-01-13 10:42:07.697][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:07.699][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-13 10:42:07.701][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:07.703][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-13 10:42:07.705][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-13 10:42:07.707][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-13 10:42:07.710][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-01-13 10:42:07.712][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-13 10:42:07.714][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:07.716][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-01-13 10:42:07.718][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-13 10:42:07.720][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:42:07.722][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:07.724][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-01-13 10:42:07.724][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-01-13 10:42:07.724][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-01-13 10:42:07.724][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-01-13 10:42:07.724][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-01-13 10:42:07.726][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-13 10:42:07.728][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:42:07.730][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:42:07.732][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-13 10:42:07.734][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:42:07.736][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:42:07.738][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-13 10:42:07.740][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:42:07.742][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-13 10:42:07.744][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-13 10:42:07.746][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-13 10:42:07.748][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:42:07.751][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-01-13 10:42:07.755][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:07.757][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-01-13 10:42:07.759][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:07.761][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-13 10:42:07.763][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:07.766][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-13 10:42:07.768][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-13 10:42:07.770][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-13 10:42:07.773][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-01-13 10:42:07.775][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-13 10:42:07.777][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-01-13 10:42:07.801][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-01-13 10:42:07.803][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-13 10:42:07.805][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:42:07.808][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:07.810][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:42:07.812][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-13 10:42:07.814][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:42:07.816][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:42:07.819][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-13 10:42:07.821][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:42:07.823][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:42:07.825][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-13 10:42:07.828][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:42:07.830][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-13 10:42:07.832][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-13 10:42:07.834][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-13 10:42:07.836][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:42:07.839][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-01-13 10:42:07.843][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:07.845][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-01-13 10:42:07.847][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:07.849][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-13 10:42:07.851][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:07.854][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-13 10:42:07.856][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-13 10:42:07.858][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-13 10:42:07.860][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-01-13 10:42:07.862][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-13 10:42:07.864][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-01-13 10:42:07.866][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-01-13 10:42:07.868][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-13 10:42:07.869][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:42:07.871][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:07.873][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:42:07.875][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-13 10:42:07.877][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:42:07.879][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:42:07.881][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-13 10:42:07.884][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:42:07.885][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:42:07.888][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-13 10:42:07.890][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:42:07.892][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-13 10:42:07.894][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-13 10:42:07.896][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-13 10:42:07.898][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:42:07.901][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-01-13 10:42:07.903][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:07.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:07.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:07.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:07.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.924][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[2022-01-13 10:42:07.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:07.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:07.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.934][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.DEBUG[2022-01-13 10:42:07.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:07.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:07.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:07.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:07.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:07.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:07.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:07.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:07.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.971][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[2022-01-13 10:42:07.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:07.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:07.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:07.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:07.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:07.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:07.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:07.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:07.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.085][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-01-13 10:42:08.089][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-01-13 10:42:08.092][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-01-13 10:42:08.096][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-01-13 10:42:08.099][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-01-13 10:42:08.102][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-01-13 10:42:08.105][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-01-13 10:42:08.109][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-01-13 10:42:08.113][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-01-13 10:42:08.142][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-01-13 10:42:08.147][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-01-13 10:42:08.151][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-01-13 10:42:08.154][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-01-13 10:42:08.158][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-01-13 10:42:08.161][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-01-13 10:42:08.164][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-01-13 10:42:08.169][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-01-13 10:42:08.172][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-01-13 10:42:08.175][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-01-13 10:42:08.184][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-01-13 10:42:08.187][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-01-13 10:42:08.190][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-01-13 10:42:08.195][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-01-13 10:42:08.198][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-01-13 10:42:08.201][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-01-13 10:42:08.206][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-01-13 10:42:08.210][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-01-13 10:42:08.213][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-01-13 10:42:08.218][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-01-13 10:42:08.221][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-01-13 10:42:08.224][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-01-13 10:42:08.228][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-01-13 10:42:08.232][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-01-13 10:42:08.235][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-01-13 10:42:08.238][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-01-13 10:42:08.241][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-01-13 10:42:08.245][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-01-13 10:42:08.248][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-01-13 10:42:08.251][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-01-13 10:42:08.255][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-01-13 10:42:08.263][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-01-13 10:42:08.266][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-01-13 10:42:08.270][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-01-13 10:42:08.275][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-01-13 10:42:08.279][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-01-13 10:42:08.282][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-01-13 10:42:08.287][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-01-13 10:42:08.291][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-01-13 10:42:08.294][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-01-13 10:42:08.300][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-01-13 10:42:08.304][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-01-13 10:42:08.307][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-01-13 10:42:08.315][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-01-13 10:42:08.319][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-01-13 10:42:08.322][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-01-13 10:42:08.327][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-01-13 10:42:08.331][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-01-13 10:42:08.334][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-01-13 10:42:08.342][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-01-13 10:42:08.345][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-01-13 10:42:08.349][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-01-13 10:42:08.354][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-01-13 10:42:08.358][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-01-13 10:42:08.361][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-01-13 10:42:08.366][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-01-13 10:42:08.370][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-01-13 10:42:08.373][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-01-13 10:42:08.379][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-01-13 10:42:08.383][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-01-13 10:42:08.387][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-01-13 10:42:08.394][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-01-13 10:42:08.398][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-01-13 10:42:08.402][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-01-13 10:42:08.407][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-01-13 10:42:08.410][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-01-13 10:42:08.413][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-01-13 10:42:08.419][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-01-13 10:42:08.422][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-01-13 10:42:08.426][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-01-13 10:42:08.431][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-01-13 10:42:08.434][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-01-13 10:42:08.437][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-01-13 10:42:08.445][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-01-13 10:42:08.449][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-01-13 10:42:08.452][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-01-13 10:42:08.458][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-01-13 10:42:08.460][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.464][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.466][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[2022-01-13 10:42:08.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:08.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:08.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.484][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[2022-01-13 10:42:08.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:08.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:08.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:08.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:08.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:08.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:08.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:08.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:08.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.581][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[2022-01-13 10:42:08.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:08.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:08.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:08.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:08.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:08.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:08.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:08.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:08.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:08.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:08.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:08.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:08.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:08.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:08.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:08.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:08.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:08.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:08.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.737][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[2022-01-13 10:42:08.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:08.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:08.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:08.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:08.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-13 10:42:08.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:08.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:08.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:08.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:08.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:08.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:08.804][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-01-13 10:42:08.808][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-01-13 10:42:08.812][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-01-13 10:42:08.815][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-01-13 10:42:08.817][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:08.825][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-13 10:42:08.827][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:08.829][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-13 10:42:08.831][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:08.833][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-13 10:42:08.838][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-01-13 10:42:08.840][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-13 10:42:08.842][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:08.844][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-01-13 10:42:08.848][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-13 10:42:08.850][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-01-13 10:42:08.850][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-01-13 10:42:08.850][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-01-13 10:42:08.850][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-01-13 10:42:08.850][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-01-13 10:42:08.850][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-01-13 10:42:08.850][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-01-13 10:42:08.850][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-01-13 10:42:08.850][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-01-13 10:42:08.852][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-01-13 10:42:08.854][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-01-13 10:42:08.854][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-01-13 10:42:08.857][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-13 10:42:08.859][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:42:08.861][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:42:08.863][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-13 10:42:08.865][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-13 10:42:08.867][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-13 10:42:08.870][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-13 10:42:08.872][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-01-13 10:42:08.872][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-01-13 10:42:08.874][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-13 10:42:08.876][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-13 10:42:08.878][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-01-13 10:42:08.881][self$setPropertyValue] 
biodb.DEBUG[2022-01-13 10:42:08.884][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-01-13 10:42:08.887][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-01-13 10:42:08.898][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-01-13 10:42:08.900][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-01-13 10:42:08.902][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-01-13 10:42:08.908][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-01-13 10:42:08.911][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-01-13 10:42:08.913][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-01-13 10:42:08.916][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-01-13 10:42:08.919][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-01-13 10:42:08.922][biodb::testThat] 
biodb.INFO [2022-01-13 10:42:08.924][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2022-01-13 10:42:08.926][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-13 10:42:08.928][biodb::testThat] 
biodb.DEBUG[2022-01-13 10:42:09.016][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[2022-01-13 10:42:09.023][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-01-13 10:42:09.026][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2022-01-13 10:42:09.028][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-01-13 10:42:09.081][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2022-01-13 10:42:10.557][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2022-01-13 10:42:10.560][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-01-13 10:42:10.563][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2022-01-13 10:42:10.567][cch$loadFileContent] file.exist = [2]: "FALSE, TRUE".
biodb.TRACE[2022-01-13 10:42:10.570][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2022-01-13 10:42:10.573][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-01-13 10:42:10.578][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-01-13 10:42:10.581][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-01-13 10:42:10.583][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-01-13 10:42:10.590][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:42:10.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:10.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:10.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:10.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:10.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:10.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-13 10:42:10.607][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2022-01-13 10:42:10.618][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-13 10:42:10.620][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-13 10:42:10.622][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2022-01-13 10:42:11.359][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.DEBUG[2022-01-13 10:42:12.105][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-01-13 10:42:12.125][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.content"
biodb.TRACE[2022-01-13 10:42:12.187][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.request"
biodb.TRACE[2022-01-13 10:42:12.213][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv"
biodb.DEBUG[2022-01-13 10:42:12.224][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-01-13 10:42:12.245][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-01-13 10:42:12.247][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-01-13 10:42:12.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:42:12.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:12.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:12.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:12.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:12.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:12.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:42:12.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:12.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:12.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:12.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:12.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-13 10:42:12.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-13 10:42:12.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.311][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-01-13 10:42:12.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-01-13 10:42:12.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.319][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-01-13 10:42:12.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-01-13 10:42:12.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.328][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:12.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:12.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.337][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:12.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:12.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.352][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:12.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:12.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.361][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:12.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:12.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.379][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-13 10:42:12.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:12.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.388][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-13 10:42:12.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:12.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.409][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:42:12.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:42:12.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.420][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:42:12.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:42:12.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.439][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:12.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:12.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.448][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:12.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:12.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.490][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-13 10:42:12.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:12.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.499][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-01-13 10:42:12.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:12.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.508][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:12.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:12.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.518][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:12.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:12.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.526][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-13 10:42:12.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:12.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:12.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:12.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.556][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:12.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:12.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.564][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:12.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:12.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:12.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:12.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:12.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:12.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.603][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:12.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:12.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.612][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:12.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:12.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:12.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:12.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.630][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:12.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:12.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:12.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:12.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:12.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:12.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:12.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:12.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-13 10:42:12.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:42:12.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:12.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:12.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:12.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:12.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:12.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:42:12.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:12.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:12.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:12.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:12.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.734][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-13 10:42:12.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-13 10:42:12.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-13 10:42:12.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-13 10:42:12.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.767][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-01-13 10:42:12.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-01-13 10:42:12.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.779][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-01-13 10:42:12.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-01-13 10:42:12.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.790][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:12.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:12.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.801][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:12.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:12.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.858][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:12.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:12.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.869][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:12.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:12.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.889][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-13 10:42:12.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:12.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.899][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-13 10:42:12.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:12.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.920][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:42:12.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:42:12.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.930][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:42:12.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:42:12.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.952][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:12.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:12.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:12.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:12.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:12.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:12.992][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-13 10:42:12.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:12.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.003][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-01-13 10:42:13.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:13.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.014][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:13.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:13.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:13.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:13.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.040][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-13 10:42:13.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:13.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.063][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.076][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:13.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:13.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.103][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:13.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:13.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:13.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:13.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:13.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:13.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:13.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:13.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:13.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:13.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:13.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:13.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:13.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:13.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:13.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:13.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:13.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:13.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-13 10:42:13.219][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2022-01-13 10:42:13.223][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2022-01-13 10:42:13.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:42:13.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:13.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:13.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:13.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:13.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:13.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:42:13.276][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-13 10:42:13.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-13 10:42:13.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.286][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-13 10:42:13.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-13 10:42:13.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.299][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-01-13 10:42:13.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-01-13 10:42:13.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.309][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-01-13 10:42:13.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-01-13 10:42:13.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.319][private$selectFields] Fields none
biodb.TRACE[2022-01-13 10:42:13.321][private$selectFields] 
biodb.TRACE[2022-01-13 10:42:13.323][private$selectFields] Fields is null: TRUE
biodb.TRACE[2022-01-13 10:42:13.325][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-13 10:42:13.331][private$selectFields] Fields [7]: "accession, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:42:13.333][ef$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:13.335][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:13.337][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.339][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.341][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:13.343][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:13.345][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.347][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.350][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:13.352][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:13.355][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.357][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.359][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:13.361][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:13.364][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.366][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.368][ef$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:42:13.370][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:42:13.374][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.376][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.378][ef$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:13.380][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:13.387][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.389][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.391][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.394][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.397][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.399][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.402][ef$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:13.404][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:13.406][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.410][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.412][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:13.415][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:13.417][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.419][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.423][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:13.426][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:13.428][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.430][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.433][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:13.436][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:13.438][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.440][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.445][ef$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:42:13.447][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:42:13.449][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.451][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.455][ef$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:13.460][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:13.462][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.464][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.466][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.470][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.472][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.474][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.476][private$selectFields] Fields [7]: "accession, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:42:13.479][private$organizeFieldsByGroups] Fields [7]: "accession, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:42:13.482][ef$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:13.485][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:13.487][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.489][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.491][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:13.494][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:13.497][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.499][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.500][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:13.503][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:13.507][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.509][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.511][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:13.513][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:13.518][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.520][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.522][ef$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:42:13.525][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:42:13.527][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.531][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.533][ef$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:13.535][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:13.537][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.539][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.543][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.545][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.547][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.549][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.552][private$organizeFieldsByGroups] Groups [2]: "c("accession", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2022-01-13 10:42:13.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:13.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:13.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:13.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:13.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:13.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:13.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.582][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:13.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:13.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.593][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:13.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:13.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.602][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:13.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:13.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.614][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:13.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:13.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.652][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:13.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:13.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.661][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:13.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:13.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:13.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:13.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:13.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:13.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:13.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:13.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.703][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:42:13.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:42:13.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.712][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:42:13.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:42:13.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.721][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:42:13.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:42:13.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.730][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:13.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:13.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.740][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:13.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:13.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.750][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:13.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:13.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.760][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.770][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.780][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.801][private$entriesToListOfDataframes] Entry converted to data frame: [1, 7]: [accession, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, ...] [LMFA00000001, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, C40H66O5, ...].
biodb.DEBUG[2022-01-13 10:42:13.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-13 10:42:13.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:13.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:13.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:13.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:13.815][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:13.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-13 10:42:13.821][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-13 10:42:13.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-13 10:42:13.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.830][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-13 10:42:13.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-13 10:42:13.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.839][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-01-13 10:42:13.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-01-13 10:42:13.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.850][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-01-13 10:42:13.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-01-13 10:42:13.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.860][private$selectFields] Fields none
biodb.TRACE[2022-01-13 10:42:13.862][private$selectFields] 
biodb.TRACE[2022-01-13 10:42:13.863][private$selectFields] Fields is null: TRUE
biodb.TRACE[2022-01-13 10:42:13.865][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-13 10:42:13.869][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:42:13.871][ef$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:13.873][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:13.875][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.877][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.879][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-13 10:42:13.881][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-13 10:42:13.884][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.886][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.888][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:13.893][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:13.895][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.897][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.899][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:13.902][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:13.904][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.906][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.908][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:13.910][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:13.913][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.915][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.918][ef$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:42:13.920][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:42:13.922][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.927][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.929][ef$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:13.932][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:13.934][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.936][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.938][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.940][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:13.942][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.944][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.949][ef$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:13.952][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:13.954][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.956][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.959][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-13 10:42:13.961][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-13 10:42:13.963][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:13.965][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:13.967][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:13.998][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:14.000][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.003][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.007][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:14.010][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:14.012][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.014][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.016][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:14.018][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:14.020][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.022][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.024][ef$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:42:14.027][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:42:14.030][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.031][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.033][ef$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:14.036][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:14.039][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.041][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.043][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:14.045][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:14.049][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.051][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.054][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:42:14.056][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-01-13 10:42:14.057][ef$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:14.059][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:14.063][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.065][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.068][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-13 10:42:14.070][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-13 10:42:14.075][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.077][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.080][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:14.082][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:14.084][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.086][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.089][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:14.091][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:14.093][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.097][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.099][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:14.101][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:14.103][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.105][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.107][ef$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:42:14.109][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:42:14.111][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.113][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.115][ef$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:14.118][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:14.121][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.123][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.125][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:14.127][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:14.131][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.133][ef$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.135][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2022-01-13 10:42:14.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:14.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:14.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:14.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:14.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-13 10:42:14.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-13 10:42:14.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-13 10:42:14.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-13 10:42:14.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-13 10:42:14.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-13 10:42:14.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-13 10:42:14.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-13 10:42:14.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.198][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:14.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:14.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.207][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:14.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:14.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.217][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:14.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-13 10:42:14.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.227][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:14.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:14.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.236][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:14.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:14.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.246][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:14.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-13 10:42:14.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:14.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:14.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:14.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:14.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:14.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-13 10:42:14.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.285][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:42:14.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:42:14.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.294][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:42:14.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:42:14.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.303][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-13 10:42:14.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-13 10:42:14.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.313][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:14.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:14.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.347][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:14.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:14.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.358][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-13 10:42:14.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-13 10:42:14.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.369][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:14.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:14.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.379][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:14.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:14.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.388][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:14.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-13 10:42:14.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-13 10:42:14.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-13 10:42:14.407][private$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[2022-01-13 10:42:14.409][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2022-01-13 10:42:14.411][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2022-01-13 10:42:14.418][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-01-13 10:42:14.420][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-01-13 10:42:14.422][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-01-13 10:42:14.424][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-01-13 10:42:14.425][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-13 10:42:14.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-13 10:42:14.430][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-13 10:42:14.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-13 10:42:14.433][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-01-13 10:42:14.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 170 ]
> 
> proc.time()
   user  system elapsed 
 32.777   1.974 122.126 

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn3.3240.6143.951
LipidmapsStructureEntry0.5340.0110.546