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This page was generated on 2022-01-17 13:07:21 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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: 2022-01-16 01:55:05 -0500 (Sun, 16 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: 2022-01-16 10:40:56 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 10:44:19 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 202.1 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 [2022-01-16 10:42:02.469][biodb::testContext] 
biodb.INFO [2022-01-16 10:42:02.484][biodb::testContext] ********************************************************************************
biodb.INFO [2022-01-16 10:42:02.486][biodb::testContext] Test context - Generic tests
biodb.INFO [2022-01-16 10:42:02.488][biodb::testContext] ********************************************************************************
biodb.INFO [2022-01-16 10:42:02.489][biodb::testContext] 
biodb.INFO [2022-01-16 10:42:02.515][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-01-16 10:42:02.518][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-01-16 10:42:02.532][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-01-16 10:42:02.534][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-01-16 10:42:02.537][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-01-16 10:42:02.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:02.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:02.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:02.545][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-01-16 10:42:02.591][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-01-16 10:42:02.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:02.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:02.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:02.599][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-01-16 10:42:02.601][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-01-16 10:42:02.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:02.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:02.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:02.609][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-01-16 10:42:02.611][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-01-16 10:42:02.613][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-01-16 10:42:02.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:02.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:02.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:02.621][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-01-16 10:42:02.623][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-01-16 10:42:02.626][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-01-16 10:42:02.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:02.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:02.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:02.634][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-01-16 10:42:02.637][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-01-16 10:42:02.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:02.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:02.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:02.644][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-01-16 10:42:02.646][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-01-16 10:42:02.648][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-01-16 10:42:02.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:02.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:02.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:02.656][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-01-16 10:42:02.658][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-01-16 10:42:02.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:02.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:02.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:02.665][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-01-16 10:42:02.667][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-01-16 10:42:02.669][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-01-16 10:42:02.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:02.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:02.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:02.674][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-01-16 10:42:02.676][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-01-16 10:42:02.678][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-01-16 10:42:02.680][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-01-16 10:42:02.682][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-01-16 10:42:02.684][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-01-16 10:42:02.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:02.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:02.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:02.690][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-01-16 10:42:02.692][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-01-16 10:42:02.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:02.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:02.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:02.698][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-01-16 10:42:02.700][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-01-16 10:42:02.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:02.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:02.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:02.706][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-01-16 10:42:02.708][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-01-16 10:42:02.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:02.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:02.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:02.715][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-01-16 10:42:02.717][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-01-16 10:42:02.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:02.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:02.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:02.724][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-01-16 10:42:02.726][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-01-16 10:42:02.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:02.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:02.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:02.732][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-01-16 10:42:02.734][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-01-16 10:42:02.745][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-01-16 10:42:02.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:02.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:02.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:02.752][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-01-16 10:42:02.754][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-01-16 10:42:02.757][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-01-16 10:42:02.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:02.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:02.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:02.770][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-01-16 10:42:02.855][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-01-16 10:42:02.884][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-01-16 10:42:02.886][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:02.888][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-16 10:42:02.890][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:02.892][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-16 10:42:02.894][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-16 10:42:02.896][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-16 10:42:02.898][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-01-16 10:42:02.900][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-16 10:42:02.902][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:02.903][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-01-16 10:42:02.905][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-16 10:42:02.907][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:42:02.909][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:02.911][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-01-16 10:42:02.911][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-01-16 10:42:02.911][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-01-16 10:42:02.911][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-01-16 10:42:02.911][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-01-16 10:42:02.912][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-16 10:42:02.914][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:42:02.915][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:42:02.917][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-16 10:42:02.918][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:42:02.920][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:42:02.921][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-16 10:42:02.923][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:42:02.925][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-16 10:42:02.926][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-16 10:42:02.928][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-16 10:42:02.930][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:42:02.933][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-01-16 10:42:02.936][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-01-16 10:42:02.938][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-01-16 10:42:02.940][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:02.942][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-16 10:42:02.944][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:02.946][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-16 10:42:02.948][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-16 10:42:02.950][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-16 10:42:02.952][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-01-16 10:42:02.954][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-16 10:42:02.956][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:02.958][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-01-16 10:42:02.960][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-16 10:42:02.961][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:42:02.963][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:02.965][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-01-16 10:42:02.965][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-01-16 10:42:02.965][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-01-16 10:42:02.965][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-01-16 10:42:02.965][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-01-16 10:42:02.967][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-16 10:42:02.969][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:42:02.971][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:42:02.973][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-16 10:42:02.974][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:42:02.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:42:02.977][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-16 10:42:02.979][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:42:02.981][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-16 10:42:02.982][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-16 10:42:02.984][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-16 10:42:02.986][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:42:02.988][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-01-16 10:42:02.992][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:02.994][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-01-16 10:42:02.996][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:02.998][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-16 10:42:03.000][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:03.002][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-16 10:42:03.003][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-16 10:42:03.005][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-16 10:42:03.006][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-01-16 10:42:03.008][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-16 10:42:03.010][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-01-16 10:42:03.012][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-01-16 10:42:03.013][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-16 10:42:03.015][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:42:03.017][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:03.019][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:42:03.021][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-16 10:42:03.023][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:42:03.024][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:42:03.026][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-16 10:42:03.028][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:42:03.029][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:42:03.031][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-16 10:42:03.033][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:42:03.035][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-16 10:42:03.037][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-16 10:42:03.038][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-16 10:42:03.040][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:42:03.043][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-01-16 10:42:03.046][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:03.049][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-01-16 10:42:03.051][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:03.053][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-16 10:42:03.055][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:03.057][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-16 10:42:03.059][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-16 10:42:03.061][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-16 10:42:03.063][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-01-16 10:42:03.065][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-16 10:42:03.067][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-01-16 10:42:03.069][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-01-16 10:42:03.071][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-16 10:42:03.073][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:42:03.075][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:03.077][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:42:03.079][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-16 10:42:03.081][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:42:03.083][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:42:03.085][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-16 10:42:03.087][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:42:03.089][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:42:03.091][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-16 10:42:03.093][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:42:03.095][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-16 10:42:03.097][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-16 10:42:03.099][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-16 10:42:03.101][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:42:03.110][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-01-16 10:42:03.112][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.151][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[2022-01-16 10:42:03.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.181][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[2022-01-16 10:42:03.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.254][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-01-16 10:42:03.265][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-01-16 10:42:03.268][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-01-16 10:42:03.271][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-01-16 10:42:03.274][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-01-16 10:42:03.276][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-01-16 10:42:03.279][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-01-16 10:42:03.282][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-01-16 10:42:03.285][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-01-16 10:42:03.289][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-01-16 10:42:03.292][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-01-16 10:42:03.296][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-01-16 10:42:03.299][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-01-16 10:42:03.310][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-01-16 10:42:03.313][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-01-16 10:42:03.315][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-01-16 10:42:03.318][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-01-16 10:42:03.321][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-01-16 10:42:03.323][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-01-16 10:42:03.325][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-01-16 10:42:03.327][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-01-16 10:42:03.329][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-01-16 10:42:03.332][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-01-16 10:42:03.334][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-01-16 10:42:03.335][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-01-16 10:42:03.338][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-01-16 10:42:03.340][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-01-16 10:42:03.343][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-01-16 10:42:03.346][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-01-16 10:42:03.349][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-01-16 10:42:03.351][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-01-16 10:42:03.354][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-01-16 10:42:03.357][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-01-16 10:42:03.360][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-01-16 10:42:03.362][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-01-16 10:42:03.364][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-01-16 10:42:03.366][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-01-16 10:42:03.369][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-01-16 10:42:03.372][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-01-16 10:42:03.374][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-01-16 10:42:03.375][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-01-16 10:42:03.378][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-01-16 10:42:03.381][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-01-16 10:42:03.384][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-01-16 10:42:03.386][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-01-16 10:42:03.387][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-01-16 10:42:03.390][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-01-16 10:42:03.392][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-01-16 10:42:03.395][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-01-16 10:42:03.397][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-01-16 10:42:03.398][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-01-16 10:42:03.400][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-01-16 10:42:03.402][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-01-16 10:42:03.405][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-01-16 10:42:03.408][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-01-16 10:42:03.410][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-01-16 10:42:03.412][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-01-16 10:42:03.415][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-01-16 10:42:03.417][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-01-16 10:42:03.420][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-01-16 10:42:03.421][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-01-16 10:42:03.424][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-01-16 10:42:03.427][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-01-16 10:42:03.430][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-01-16 10:42:03.433][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-01-16 10:42:03.436][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-01-16 10:42:03.438][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-01-16 10:42:03.441][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-01-16 10:42:03.442][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-01-16 10:42:03.445][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-01-16 10:42:03.447][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-01-16 10:42:03.449][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-01-16 10:42:03.451][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-01-16 10:42:03.453][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-01-16 10:42:03.456][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-01-16 10:42:03.458][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-01-16 10:42:03.461][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-01-16 10:42:03.464][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-01-16 10:42:03.467][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-01-16 10:42:03.468][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-01-16 10:42:03.470][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-01-16 10:42:03.472][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-01-16 10:42:03.473][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-01-16 10:42:03.484][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-01-16 10:42:03.486][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-01-16 10:42:03.491][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-01-16 10:42:03.492][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.495][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:03.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:03.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:03.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:03.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:03.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:03.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:03.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:03.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:03.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:03.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:03.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:03.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:03.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:03.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.571][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[2022-01-16 10:42:03.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:03.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:03.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:03.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:03.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:03.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:03.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:03.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:03.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:03.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:03.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:03.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:03.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.631][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[2022-01-16 10:42:03.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:03.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:03.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:03.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:03.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:03.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:03.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:42:03.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:03.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:03.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:03.672][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-01-16 10:42:03.691][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-01-16 10:42:03.695][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-01-16 10:42:03.703][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-01-16 10:42:03.705][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:03.706][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-16 10:42:03.707][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:03.708][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-16 10:42:03.710][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:03.712][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-16 10:42:03.714][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-01-16 10:42:03.716][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-16 10:42:03.718][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:03.720][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-01-16 10:42:03.721][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-16 10:42:03.723][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-01-16 10:42:03.723][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-01-16 10:42:03.723][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-01-16 10:42:03.723][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-01-16 10:42:03.723][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-01-16 10:42:03.723][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-01-16 10:42:03.723][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-01-16 10:42:03.723][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-01-16 10:42:03.723][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-01-16 10:42:03.725][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-01-16 10:42:03.727][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-01-16 10:42:03.727][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-01-16 10:42:03.729][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-16 10:42:03.730][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:42:03.732][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:42:03.733][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-16 10:42:03.735][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:42:03.737][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:42:03.739][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-16 10:42:03.741][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-01-16 10:42:03.741][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-01-16 10:42:03.742][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-16 10:42:03.744][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-16 10:42:03.746][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-01-16 10:42:03.748][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:42:03.757][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-01-16 10:42:03.759][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-01-16 10:42:03.791][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-01-16 10:42:03.793][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-01-16 10:42:03.801][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-01-16 10:42:03.807][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-01-16 10:42:03.816][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-01-16 10:42:03.818][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-01-16 10:42:03.820][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-01-16 10:42:03.822][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-01-16 10:42:03.851][biodb::testThat] 
biodb.INFO [2022-01-16 10:42:03.852][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2022-01-16 10:42:03.854][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:42:03.855][biodb::testThat] 
biodb.TRACE[2022-01-16 10:42:03.859][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[2022-01-16 10:42:03.869][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-01-16 10:42:03.872][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-01-16 10:42:03.887][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:42:03.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:03.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:03.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:03.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:03.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:03.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-16 10:42:03.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:03.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:03.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:03.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:03.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:03.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:03.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:03.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:03.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-16 10:42:03.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-16 10:42:03.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:03.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:03.974][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-01-16 10:42:03.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-01-16 10:42:03.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:03.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:03.981][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-01-16 10:42:03.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-01-16 10:42:03.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:03.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:03.989][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:03.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:03.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:03.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.053][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:04.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:04.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.068][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:04.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:04.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.076][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:04.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:04.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.091][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-16 10:42:04.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:04.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.100][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-16 10:42:04.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:04.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.115][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:42:04.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:42:04.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.124][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:42:04.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:42:04.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.136][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:04.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:04.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.143][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:04.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:04.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.170][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-16 10:42:04.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:04.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.178][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-01-16 10:42:04.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:04.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:04.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:04.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.190][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:04.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:04.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.198][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-16 10:42:04.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:04.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.242][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:04.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:04.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.249][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:04.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:04.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.318][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:04.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:04.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.326][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:04.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:04.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.333][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:04.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:04.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.346][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:04.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:04.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.355][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:04.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:04.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.367][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:04.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:04.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-16 10:42:04.423][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2022-01-16 10:42:04.433][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-16 10:42:04.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-16 10:42:04.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.439][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-16 10:42:04.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-16 10:42:04.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.447][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-01-16 10:42:04.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-01-16 10:42:04.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.455][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-01-16 10:42:04.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-01-16 10:42:04.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.542][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:04.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:04.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.598][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:04.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:04.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.606][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:04.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:04.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.613][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:04.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:04.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.648][ef$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.651][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.652][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.654][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:04.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:04.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.679][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:04.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:04.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.687][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:04.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:04.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.693][ef$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:04.695][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:04.697][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.699][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:04.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:04.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.717][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:04.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:04.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.724][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:04.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:04.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.731][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:04.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:04.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.737][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:04.739][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:04.740][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.741][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.743][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:04.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:04.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.761][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:42:04.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:42:04.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.768][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:42:04.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:42:04.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.775][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:42:04.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:42:04.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.784][ef$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:42:04.786][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:42:04.788][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.789][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.791][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:42:04.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:42:04.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:04.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:04.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:04.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:04.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:04.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:04.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.832][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:04.834][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:04.836][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.838][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:04.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:04.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.855][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:04.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:04.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.863][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:04.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:04.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.871][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:04.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:04.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.878][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:04.880][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:04.881][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.883][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.885][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:04.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:04.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.901][ef$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:04.903][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:04.905][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.907][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.913][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:04.915][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:04.917][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.919][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.925][ef$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:42:04.927][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:42:04.929][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.931][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.944][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:04.946][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:04.948][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.949][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.955][ef$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:04.956][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:04.958][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.960][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:04.965][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:04.967][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:04.968][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:04.970][ef$get] fields variable is a list.
biodb.INFO [2022-01-16 10:42:04.977][biodb::testThat] 
biodb.INFO [2022-01-16 10:42:04.978][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2022-01-16 10:42:04.980][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:42:04.982][biodb::testThat] 
biodb.DEBUG[2022-01-16 10:42:05.007][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2022-01-16 10:42:05.021][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2022-01-16 10:42:05.027][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2022-01-16 10:42:05.029][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-01-16 10:42:05.032][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2022-01-16 10:42:05.034][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-01-16 10:42:05.106][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-01-16 10:42:05.108][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-01-16 10:42:05.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:42:05.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:05.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:05.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:05.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:05.119][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:05.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-16 10:42:05.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:05.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:05.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:05.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:05.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-16 10:42:05.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-16 10:42:05.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.162][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-01-16 10:42:05.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-01-16 10:42:05.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.169][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-01-16 10:42:05.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-01-16 10:42:05.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.177][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:05.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:05.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.186][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:05.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:05.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.201][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:05.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:05.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.208][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:05.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:05.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.221][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-16 10:42:05.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:05.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.229][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-16 10:42:05.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:05.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.246][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:42:05.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:42:05.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.254][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:42:05.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:42:05.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.269][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:05.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.276][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:05.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.289][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-16 10:42:05.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.298][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-01-16 10:42:05.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.305][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:05.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.312][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:05.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.320][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-16 10:42:05.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.342][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:05.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.349][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:05.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.357][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:05.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.364][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:05.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.371][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:05.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.382][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:05.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:05.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.389][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:05.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:05.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:05.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:05.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.404][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:05.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:05.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:05.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:05.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:05.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:05.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:05.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:05.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:05.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:05.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:05.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:05.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:05.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:05.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-16 10:42:05.460][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2022-01-16 10:42:05.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-01-16 10:42:05.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-01-16 10:42:05.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-01-16 10:42:05.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-01-16 10:42:05.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-01-16 10:42:05.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-01-16 10:42:05.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-01-16 10:42:05.491][biodb::testThat] 
biodb.INFO [2022-01-16 10:42:05.493][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2022-01-16 10:42:05.495][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:42:05.496][biodb::testThat] 
biodb.TRACE[2022-01-16 10:42:05.500][ef$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:05.502][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.504][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.505][ef$get] fields variable is a list.
biodb.DEBUG[2022-01-16 10:42:05.507][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2022-01-16 10:42:05.545][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:05.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.553][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:05.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:05.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-16 10:42:05.571][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-01-16 10:42:05.620][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[2022-01-16 10:42:05.655][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-01-16 10:42:05.722][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-01-16 10:42:05.724][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-01-16 10:42:05.727][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2022-01-16 10:42:05.730][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2022-01-16 10:42:05.743][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:05.745][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:05.747][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.749][ef$get] fields variable is a list.
biodb.INFO [2022-01-16 10:42:05.752][biodb::testThat] 
biodb.INFO [2022-01-16 10:42:05.754][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2022-01-16 10:42:05.756][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:42:05.758][biodb::testThat] 
biodb.TRACE[2022-01-16 10:42:05.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:05.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:05.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:05.798][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:05.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:05.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:05.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-16 10:42:06.034][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[2022-01-16 10:42:06.041][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-01-16 10:42:06.044][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-01-16 10:42:06.046][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-01-16 10:42:06.049][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2022-01-16 10:42:06.068][biodb::testThat] 
biodb.INFO [2022-01-16 10:42:06.070][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2022-01-16 10:42:06.072][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:42:06.073][biodb::testThat] 
biodb.TRACE[2022-01-16 10:42:06.132][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-16 10:42:06.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-16 10:42:06.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:06.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:06.140][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-16 10:42:06.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-16 10:42:06.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:06.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:06.149][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-01-16 10:42:06.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-01-16 10:42:06.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:06.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:06.157][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-01-16 10:42:06.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-01-16 10:42:06.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:06.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:06.256][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-16 10:42:06.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-16 10:42:06.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:06.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:06.264][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-16 10:42:06.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-16 10:42:06.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:06.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:06.272][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-01-16 10:42:06.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-01-16 10:42:06.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:06.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:06.280][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-01-16 10:42:06.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-01-16 10:42:06.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:06.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-01-16 10:42:06.293][biodb::testThat] 
biodb.INFO [2022-01-16 10:42:06.295][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2022-01-16 10:42:06.296][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:42:06.298][biodb::testThat] 
biodb.INFO [2022-01-16 10:42:06.306][biodb::testThat] 
biodb.INFO [2022-01-16 10:42:06.308][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2022-01-16 10:42:06.310][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:42:06.312][biodb::testThat] 
biodb.INFO [2022-01-16 10:42:06.319][biodb::testThat] 
biodb.INFO [2022-01-16 10:42:06.321][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2022-01-16 10:42:06.323][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:42:06.324][biodb::testThat] 
biodb.DEBUG[2022-01-16 10:42:06.328][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2022-01-16 10:42:07.507][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2022-01-16 10:42:07.925][biodb::testThat] 
biodb.INFO [2022-01-16 10:42:07.926][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2022-01-16 10:42:07.927][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:42:07.928][biodb::testThat] 
biodb.INFO [2022-01-16 10:42:07.933][biodb::testThat] 
biodb.INFO [2022-01-16 10:42:07.935][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2022-01-16 10:42:07.937][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:42:07.939][biodb::testThat] 
biodb.TRACE[2022-01-16 10:42:07.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:07.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:07.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:07.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:07.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:07.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:07.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:07.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:07.965][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:07.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:07.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:07.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-16 10:42:08.105][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.INFO [2022-01-16 10:42:08.111][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.DEBUG[2022-01-16 10:42:08.113][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:42:08.115][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:42:08.118][private$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[2022-01-16 10:42:08.881][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[2022-01-16 10:42:09.658][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-16 10:42:09.695][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2022-01-16 10:42:09.781][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2022-01-16 10:42:09.832][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-01-16 10:42:09.838][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-01-16 10:42:09.841][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-01-16 10:42:09.843][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-01-16 10:42:09.845][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2022-01-16 10:42:09.861][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-01-16 10:42:09.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-01-16 10:42:09.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:09.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:09.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-01-16 10:42:09.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-01-16 10:42:09.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:09.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:09.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:09.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:09.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:09.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:09.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:09.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:09.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:09.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:09.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:09.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:09.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:09.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:09.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:09.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:09.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:09.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:09.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:09.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:09.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:09.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-16 10:42:09.973][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[2022-01-16 10:42:10.007][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:42:10.009][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:42:10.054][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2022-01-16 10:42:14.438][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2022-01-16 10:42:20.399][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-16 10:42:20.408][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2022-01-16 10:42:20.520][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2022-01-16 10:42:21.102][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2022-01-16 10:42:21.108][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:42:21.110][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:42:21.113][private$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[2022-01-16 10:42:21.749][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[2022-01-16 10:42:22.393][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-16 10:42:22.403][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2022-01-16 10:42:22.418][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2022-01-16 10:42:22.481][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[2022-01-16 10:42:22.487][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:42:22.489][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:42:22.492][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2022-01-16 10:42:23.130][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2022-01-16 10:42:24.173][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-16 10:42:24.183][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2022-01-16 10:42:24.198][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2022-01-16 10:42:24.222][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-01-16 10:42:24.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-01-16 10:42:24.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:24.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-01-16 10:42:24.237][biodb::testThat] 
biodb.INFO [2022-01-16 10:42:24.239][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2022-01-16 10:42:24.241][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:42:24.243][biodb::testThat] 
biodb.TRACE[2022-01-16 10:42:24.248][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-01-16 10:42:24.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-01-16 10:42:24.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:24.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:24.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-01-16 10:42:24.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-01-16 10:42:24.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:24.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:24.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:24.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:24.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:24.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:24.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:24.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:24.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:24.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:24.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:24.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:24.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:24.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:24.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:24.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:24.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:24.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-16 10:42:24.299][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:42:24.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:24.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:24.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:24.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:24.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:24.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:24.449][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2022-01-16 10:42:24.454][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:42:24.457][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:42:24.460][private$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[2022-01-16 10:42:28.890][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[2022-01-16 10:42:35.117][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-16 10:42:35.132][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2022-01-16 10:42:35.233][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2022-01-16 10:42:35.691][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2022-01-16 10:42:35.777][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-01-16 10:42:35.780][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2022-01-16 10:42:35.783][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2022-01-16 10:42:35.785][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-01-16 10:42:35.787][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-01-16 10:42:35.789][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-01-16 10:42:35.791][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-01-16 10:42:35.793][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-01-16 10:42:35.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:42:35.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:35.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:35.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:35.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:35.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:35.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:35.835][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2022-01-16 10:42:35.841][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:42:35.843][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:42:35.845][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2022-01-16 10:42:36.538][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2022-01-16 10:42:37.229][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-01-16 10:42:37.404][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2022-01-16 10:42:37.428][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2022-01-16 10:42:37.439][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:42:37.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:37.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:37.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:37.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:37.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:37.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:37.449][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2022-01-16 10:42:37.455][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:42:37.456][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:42:37.458][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2022-01-16 10:42:38.114][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2022-01-16 10:42:38.869][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-01-16 10:42:38.886][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2022-01-16 10:42:38.910][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2022-01-16 10:42:38.934][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2022-01-16 10:42:38.942][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-01-16 10:42:38.961][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-01-16 10:42:38.963][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-01-16 10:42:38.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:42:38.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:38.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:38.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:38.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:38.978][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:38.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-16 10:42:38.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:38.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:38.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:38.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:38.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:38.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:39.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-16 10:42:39.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-16 10:42:39.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-16 10:42:39.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-16 10:42:39.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.035][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-01-16 10:42:39.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-01-16 10:42:39.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.043][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-01-16 10:42:39.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-01-16 10:42:39.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.051][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:39.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:39.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.060][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:39.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:39.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.076][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:39.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:39.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.086][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:39.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:39.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.100][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-16 10:42:39.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:39.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.106][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-16 10:42:39.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:39.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.136][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:42:39.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:42:39.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.144][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:42:39.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:42:39.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.159][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:39.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:39.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.166][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:39.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:39.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.179][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-16 10:42:39.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:39.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.186][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-01-16 10:42:39.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:39.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.194][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:39.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:39.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.202][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:39.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:39.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.209][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-16 10:42:39.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:39.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.223][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.231][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:39.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:39.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.246][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:39.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:39.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:39.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:39.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:39.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:39.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-16 10:42:39.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:42:39.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:39.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:39.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:39.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:39.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:39.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-16 10:42:39.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:39.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:39.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:39.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:39.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-16 10:42:39.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-16 10:42:39.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.329][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-01-16 10:42:39.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-01-16 10:42:39.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.335][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-01-16 10:42:39.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-01-16 10:42:39.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.341][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:39.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:39.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.349][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:39.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:42:39.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.365][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:39.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:39.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.371][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:39.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:42:39.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.382][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-16 10:42:39.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:39.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.404][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-16 10:42:39.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:39.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.416][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:42:39.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:42:39.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.424][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:42:39.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:42:39.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.437][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:39.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:39.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:39.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:39.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.460][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-16 10:42:39.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:39.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.468][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-01-16 10:42:39.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:39.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.475][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:39.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:39.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.482][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:42:39.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:39.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.491][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-16 10:42:39.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:42:39.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.506][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.513][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:39.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:39.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.531][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:39.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:39.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:39.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:39.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:39.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:39.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:39.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:39.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:39.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:39.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:39.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:39.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:39.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:39.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:39.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:39.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:42:39.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:42:39.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-16 10:42:39.616][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2022-01-16 10:42:39.638][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-01-16 10:42:39.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:42:39.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:39.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:39.648][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:39.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:39.651][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:39.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-16 10:42:39.656][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.664][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.673][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:39.676][private$selectFields] 
biodb.TRACE[2022-01-16 10:42:39.678][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-01-16 10:42:39.680][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-16 10:42:39.682][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:39.684][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.706][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.708][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.710][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.712][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.714][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.716][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.718][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.720][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:39.722][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:39.724][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.727][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.729][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.731][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.733][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-01-16 10:42:39.735][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.741][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.748][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.764][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-01-16 10:42:39.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:42:39.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:39.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:39.769][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:39.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:39.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:39.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-16 10:42:39.775][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.782][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.790][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:39.792][private$selectFields] 
biodb.TRACE[2022-01-16 10:42:39.794][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-01-16 10:42:39.796][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-16 10:42:39.798][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:39.799][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.800][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.802][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.804][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.806][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.808][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.810][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.812][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.814][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:39.816][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:39.818][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.820][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.822][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.824][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.825][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-01-16 10:42:39.827][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.836][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.845][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.851][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-01-16 10:42:39.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:42:39.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:39.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:39.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:39.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:39.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:39.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-16 10:42:39.866][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.875][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.884][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:39.886][private$selectFields] 
biodb.TRACE[2022-01-16 10:42:39.887][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-01-16 10:42:39.889][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-16 10:42:39.890][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:39.891][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.894][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.896][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.898][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.900][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.902][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.904][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.906][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.908][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:39.910][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:39.912][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.915][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.916][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.917][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.919][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-01-16 10:42:39.920][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.928][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.936][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:39.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:39.944][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-01-16 10:42:39.945][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-01-16 10:42:39.946][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-01-16 10:42:39.959][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-01-16 10:42:39.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-01-16 10:42:39.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:39.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-01-16 10:42:39.991][biodb::testThat] 
biodb.INFO [2022-01-16 10:42:39.993][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2022-01-16 10:42:39.995][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:42:39.997][biodb::testThat] 
biodb.TRACE[2022-01-16 10:42:40.001][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-01-16 10:42:40.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-01-16 10:42:40.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:40.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:40.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-01-16 10:42:40.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-01-16 10:42:40.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:40.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:40.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:40.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:40.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:40.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:40.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:40.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:40.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:40.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:40.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:40.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:40.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:40.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:40.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:40.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:40.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:40.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-16 10:42:40.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:42:40.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:40.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:40.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:40.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:40.167][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:40.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:40.311][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2022-01-16 10:42:40.316][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:42:40.317][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:42:40.320][private$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[2022-01-16 10:42:44.973][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[2022-01-16 10:42:50.995][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2022-01-16 10:42:51.006][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2022-01-16 10:42:51.015][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2022-01-16 10:42:51.128][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2022-01-16 10:42:51.645][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-01-16 10:42:51.695][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:42:51.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:51.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:51.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:51.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:51.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:51.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-16 10:42:51.734][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:51.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:51.742][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:51.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:51.819][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:51.821][private$selectFields] 
biodb.TRACE[2022-01-16 10:42:51.823][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-01-16 10:42:51.825][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-16 10:42:51.826][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:51.828][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.829][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.831][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:51.833][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:51.835][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.836][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.838][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:51.840][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:51.842][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:51.863][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:51.865][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.868][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.870][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:51.872][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:51.874][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-01-16 10:42:51.876][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:51.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:51.884][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:51.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:51.893][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:51.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:51.902][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-01-16 10:42:51.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:42:51.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:51.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:51.911][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:51.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:51.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:51.915][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.TRACE[2022-01-16 10:42:51.917][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:51.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:51.925][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:51.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:51.932][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:51.935][private$selectFields] 
biodb.TRACE[2022-01-16 10:42:51.937][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-01-16 10:42:51.939][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-16 10:42:51.941][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:51.943][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.945][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.947][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:51.949][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:51.950][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.952][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.954][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:51.955][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:51.957][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:51.958][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:51.960][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.962][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.964][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:51.965][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:51.967][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-01-16 10:42:51.968][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:51.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:51.974][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:51.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:51.981][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:51.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:51.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:51.989][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-01-16 10:42:51.991][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:42:51.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:51.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:51.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:52.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:52.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:52.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-16 10:42:52.007][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:52.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:52.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:52.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:52.017][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:52.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:52.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:52.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:52.025][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:52.027][private$selectFields] 
biodb.TRACE[2022-01-16 10:42:52.029][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-01-16 10:42:52.031][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-16 10:42:52.033][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:52.035][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:52.037][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:52.039][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:52.041][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:52.042][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:52.044][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:52.046][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:52.048][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:52.050][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:52.052][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:42:52.054][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:52.056][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:52.058][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:52.059][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:52.061][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-01-16 10:42:52.063][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:52.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:52.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:52.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:52.072][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:52.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:52.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:52.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:52.096][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:52.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:42:52.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:52.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:52.103][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-01-16 10:42:52.104][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-01-16 10:42:52.106][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-01-16 10:42:52.116][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-01-16 10:42:52.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-01-16 10:42:52.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:52.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-01-16 10:42:52.126][biodb::testThat] 
biodb.INFO [2022-01-16 10:42:52.128][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2022-01-16 10:42:52.130][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:42:52.132][biodb::testThat] 
biodb.TRACE[2022-01-16 10:42:52.138][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-01-16 10:42:52.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-01-16 10:42:52.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:52.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:52.146][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-01-16 10:42:52.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-01-16 10:42:52.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:52.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:52.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:52.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:52.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:52.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:52.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:52.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:52.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:52.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:52.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:52.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:52.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:52.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:42:52.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:52.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:42:52.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:42:52.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-16 10:42:52.191][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:42:52.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:42:52.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:42:52.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:42:52.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:42:52.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:42:52.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:42:52.337][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2022-01-16 10:42:52.342][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:42:52.343][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:42:52.345][private$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[2022-01-16 10:42:56.810][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[2022-01-16 10:43:02.882][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-16 10:43:02.897][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2022-01-16 10:43:02.975][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2022-01-16 10:43:03.437][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-01-16 10:43:03.439][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:43:03.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:03.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:03.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:03.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:03.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:03.448][FUN] Functions in observer BiodbConfig: [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[2022-01-16 10:43:03.451][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.458][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.467][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:43:03.469][private$selectFields] 
biodb.TRACE[2022-01-16 10:43:03.471][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-01-16 10:43:03.473][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-16 10:43:03.475][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:43:03.477][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.479][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.481][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.483][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.485][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.487][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.489][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.491][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.492][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:43:03.494][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:43:03.496][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.498][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.500][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.502][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.503][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-01-16 10:43:03.505][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.513][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.519][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.526][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-01-16 10:43:03.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:43:03.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:03.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:03.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:03.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:03.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:03.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-16 10:43:03.536][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.541][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.546][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:43:03.547][private$selectFields] 
biodb.TRACE[2022-01-16 10:43:03.549][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-01-16 10:43:03.551][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-16 10:43:03.553][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:43:03.555][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.556][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.558][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.559][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.560][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.561][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.562][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.563][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.565][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:43:03.566][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:43:03.567][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.568][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.569][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.570][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.572][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-01-16 10:43:03.573][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.577][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.582][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.587][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-01-16 10:43:03.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:43:03.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:03.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:03.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:03.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:03.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:03.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-16 10:43:03.597][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.602][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.634][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:43:03.637][private$selectFields] 
biodb.TRACE[2022-01-16 10:43:03.639][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-01-16 10:43:03.641][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-16 10:43:03.643][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:43:03.644][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.646][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.647][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.649][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.651][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.654][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.656][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.657][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.659][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:43:03.662][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:43:03.663][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.665][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.666][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.667][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.669][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-01-16 10:43:03.671][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.681][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.691][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:03.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:03.696][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-01-16 10:43:03.697][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-01-16 10:43:03.699][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-01-16 10:43:03.723][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-01-16 10:43:03.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-01-16 10:43:03.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:03.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-01-16 10:43:03.729][biodb::testThat] 
biodb.INFO [2022-01-16 10:43:03.731][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2022-01-16 10:43:03.733][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:43:03.734][biodb::testThat] 
biodb.DEBUG[2022-01-16 10:43:03.736][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2022-01-16 10:43:03.738][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2022-01-16 10:43:03.742][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2022-01-16 10:43:03.744][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-01-16 10:43:03.747][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-01-16 10:43:03.748][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-01-16 10:43:03.749][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-01-16 10:43:03.751][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-01-16 10:43:03.752][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-01-16 10:43:03.769][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:43:03.770][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:03.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:03.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:03.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:03.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:03.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:03.781][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2022-01-16 10:43:03.785][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:03.786][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:03.788][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-16 10:43:04.393][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:04.394][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:04.396][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[2022-01-16 10:43:04.399][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-16 10:43:05.118][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-01-16 10:43:05.120][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:05.121][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:05.122][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-16 10:43:05.800][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:05.802][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:05.804][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[2022-01-16 10:43:05.806][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-16 10:43:06.870][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-01-16 10:43:06.872][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:06.873][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:06.875][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-16 10:43:07.514][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:07.516][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:07.517][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[2022-01-16 10:43:07.519][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-16 10:43:08.218][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-01-16 10:43:08.219][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:08.220][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:08.222][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-16 10:43:08.845][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:08.847][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:08.849][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[2022-01-16 10:43:08.850][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-16 10:43:09.754][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-01-16 10:43:09.756][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:09.759][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:09.761][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-16 10:43:10.379][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:10.381][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:10.383][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-16 10:43:10.386][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-16 10:43:11.342][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-01-16 10:43:11.344][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:11.345][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:11.348][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-16 10:43:12.014][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:12.016][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:12.018][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[2022-01-16 10:43:12.020][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-16 10:43:12.825][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-01-16 10:43:12.826][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:12.827][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:12.830][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-16 10:43:13.471][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:13.472][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:13.474][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[2022-01-16 10:43:13.476][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-16 10:43:14.202][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-01-16 10:43:14.204][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:14.206][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:14.208][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-16 10:43:14.867][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:14.869][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:14.871][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[2022-01-16 10:43:14.873][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-16 10:43:15.798][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-01-16 10:43:15.800][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:15.801][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:15.804][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-16 10:43:16.414][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:16.415][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:16.417][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[2022-01-16 10:43:16.419][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-16 10:43:17.133][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-01-16 10:43:17.135][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:17.136][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:17.137][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-01-16 10:43:17.760][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:17.762][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:17.764][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[2022-01-16 10:43:17.766][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-01-16 10:43:18.670][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2022-01-16 10:43:18.699][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2022-01-16 10:43:18.705][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-01-16 10:43:18.717][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-01-16 10:43:18.718][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-01-16 10:43:18.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:43:18.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:18.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:18.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:18.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:18.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:18.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-16 10:43:18.729][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:18.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:18.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:18.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:18.735][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:18.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:18.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:18.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:18.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:18.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:18.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:18.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:18.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:18.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:18.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:18.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:18.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:18.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:18.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:18.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:18.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:18.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:18.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:18.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:18.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:18.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:18.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:18.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:18.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:18.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:18.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:18.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-16 10:43:18.772][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2022-01-16 10:43:18.773][self$createEntryFromContent] Found %d entry/ies without an accession number. Set it/them to NULL.1
biodb.INFO [2022-01-16 10:43:18.777][biodb::testThat] 
biodb.INFO [2022-01-16 10:43:18.779][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2022-01-16 10:43:18.780][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:43:18.781][biodb::testThat] 
biodb.DEBUG[2022-01-16 10:43:18.790][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2022-01-16 10:43:18.792][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2022-01-16 10:43:18.794][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-01-16 10:43:18.797][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2022-01-16 10:43:18.800][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2022-01-16 10:43:18.802][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-01-16 10:43:18.803][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-01-16 10:43:18.804][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-01-16 10:43:18.806][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-01-16 10:43:18.808][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-01-16 10:43:18.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:43:18.815][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:18.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:18.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:18.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:18.824][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:18.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:18.828][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2022-01-16 10:43:18.833][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:18.835][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:18.838][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-16 10:43:19.457][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:19.458][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:19.460][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-16 10:43:19.462][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-16 10:43:20.191][private$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[2022-01-16 10:43:20.247][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:20.249][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:20.251][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-16 10:43:20.888][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:20.890][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:20.892][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-16 10:43:20.894][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-16 10:43:21.710][private$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[2022-01-16 10:43:21.712][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:21.714][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:21.716][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-16 10:43:22.357][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:22.359][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:22.361][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-16 10:43:22.363][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-16 10:43:23.112][private$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[2022-01-16 10:43:23.114][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:23.116][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:23.119][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-16 10:43:23.747][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:23.749][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:23.751][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-16 10:43:23.754][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-16 10:43:24.583][private$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[2022-01-16 10:43:24.585][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:24.587][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:24.589][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-16 10:43:25.233][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:25.235][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:25.237][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-16 10:43:25.239][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-16 10:43:26.056][private$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[2022-01-16 10:43:26.058][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:26.060][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:26.062][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-16 10:43:26.687][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:26.688][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:26.690][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-16 10:43:26.693][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-16 10:43:27.554][private$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[2022-01-16 10:43:27.557][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:27.559][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:27.562][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-16 10:43:28.202][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:28.204][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:28.206][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-16 10:43:28.208][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-16 10:43:29.376][private$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[2022-01-16 10:43:29.378][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:29.379][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:29.380][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-16 10:43:30.007][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:30.008][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:30.010][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-16 10:43:30.012][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-16 10:43:30.856][private$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[2022-01-16 10:43:30.858][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:30.860][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:30.863][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-16 10:43:31.488][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:31.489][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:31.490][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-16 10:43:31.492][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-16 10:43:32.204][private$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[2022-01-16 10:43:32.206][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:32.208][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:32.210][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-01-16 10:43:32.838][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-01-16 10:43:32.840][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-01-16 10:43:32.842][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-01-16 10:43:32.844][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-01-16 10:43:33.804][private$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[2022-01-16 10:43:33.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:43:33.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:33.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:33.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:33.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:33.813][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:33.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:33.815][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2022-01-16 10:43:33.820][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:33.821][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:33.823][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2022-01-16 10:43:34.485][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2022-01-16 10:43:35.229][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-01-16 10:43:35.247][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2022-01-16 10:43:35.270][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2022-01-16 10:43:35.292][private$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[2022-01-16 10:43:35.300][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-01-16 10:43:35.338][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-01-16 10:43:35.341][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-01-16 10:43:35.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:43:35.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:35.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:35.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:35.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:35.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:35.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-16 10:43:35.357][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:35.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:35.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.363][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:35.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:35.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:35.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:35.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-16 10:43:35.375][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:43:35.376][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:35.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:35.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:35.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:35.382][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:35.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-16 10:43:35.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:35.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:35.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:35.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:35.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-16 10:43:35.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-16 10:43:35.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-16 10:43:35.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-16 10:43:35.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.422][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-01-16 10:43:35.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-01-16 10:43:35.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.428][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-01-16 10:43:35.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-01-16 10:43:35.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.442][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-01-16 10:43:35.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-01-16 10:43:35.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.450][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-01-16 10:43:35.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-01-16 10:43:35.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.466][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:43:35.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:43:35.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.475][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:43:35.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:43:35.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.491][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:43:35.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:43:35.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.496][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:43:35.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:43:35.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.510][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-16 10:43:35.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:43:35.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.518][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-16 10:43:35.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:43:35.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.534][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:43:35.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:43:35.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.542][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:43:35.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:43:35.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.557][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:43:35.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:43:35.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.565][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:43:35.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:43:35.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.599][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-16 10:43:35.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:43:35.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.607][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-01-16 10:43:35.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:43:35.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:43:35.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:43:35.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.618][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:43:35.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:43:35.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.625][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-16 10:43:35.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:43:35.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.641][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:43:35.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:43:35.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.649][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:43:35.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:43:35.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.655][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:43:35.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:43:35.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.660][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:43:35.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:43:35.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:43:35.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:43:35.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.678][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:35.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:35.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.686][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:35.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:35.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:35.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:35.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.702][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:35.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:43:35.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:35.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:35.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:35.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:35.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:35.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:35.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:35.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:35.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:35.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:35.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:35.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:35.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:35.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:35.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:35.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:35.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:35.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:35.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:35.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:35.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:43:35.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:43:35.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:43:35.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:43:35.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-16 10:43:35.790][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2022-01-16 10:43:35.791][self$createEntryFromContent] Found %d entry/ies without an accession number. Set it/them to NULL.1
biodb.DEBUG[2022-01-16 10:43:35.793][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2022-01-16 10:43:35.806][biodb::testThat] 
biodb.INFO [2022-01-16 10:43:35.808][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2022-01-16 10:43:35.810][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:43:35.811][biodb::testThat] 
biodb.INFO [2022-01-16 10:43:35.859][biodb::testThat] 
biodb.INFO [2022-01-16 10:43:35.860][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2022-01-16 10:43:35.861][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:43:35.862][biodb::testThat] 
biodb.INFO [2022-01-16 10:43:35.868][biodb::testThat] 
biodb.INFO [2022-01-16 10:43:35.869][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2022-01-16 10:43:35.870][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:43:35.872][biodb::testThat] 
biodb.DEBUG[2022-01-16 10:43:35.901][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2022-01-16 10:43:35.905][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:35.906][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:35.908][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2022-01-16 10:43:40.365][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2022-01-16 10:43:46.342][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-16 10:43:46.365][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2022-01-16 10:43:46.455][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.INFO [2022-01-16 10:43:46.975][biodb::testThat] 
biodb.INFO [2022-01-16 10:43:46.976][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2022-01-16 10:43:46.977][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:43:46.979][biodb::testThat] 
biodb.ERROR[2022-01-16 10:43:46.997][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2022-01-16 10:43:47.019][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2022-01-16 10:43:47.033][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-01-16 10:43:47.035][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-01-16 10:43:47.037][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-01-16 10:43:47.039][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-01-16 10:43:47.041][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:47.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:47.045][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.049][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.050][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.INFO [2022-01-16 10:43:47.059][biodb::testContext] 
biodb.INFO [2022-01-16 10:43:47.061][biodb::testContext] ********************************************************************************
biodb.INFO [2022-01-16 10:43:47.063][biodb::testContext] Test context - Web services tests
biodb.INFO [2022-01-16 10:43:47.065][biodb::testContext] ********************************************************************************
biodb.INFO [2022-01-16 10:43:47.066][biodb::testContext] 
biodb.INFO [2022-01-16 10:43:47.077][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-01-16 10:43:47.080][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-01-16 10:43:47.088][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-01-16 10:43:47.090][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-01-16 10:43:47.093][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-01-16 10:43:47.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.100][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-01-16 10:43:47.102][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-01-16 10:43:47.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.109][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-01-16 10:43:47.110][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-01-16 10:43:47.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.117][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-01-16 10:43:47.119][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-01-16 10:43:47.121][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-01-16 10:43:47.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.127][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-01-16 10:43:47.128][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-01-16 10:43:47.130][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-01-16 10:43:47.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.138][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-01-16 10:43:47.140][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-01-16 10:43:47.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.150][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-01-16 10:43:47.152][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-01-16 10:43:47.154][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-01-16 10:43:47.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.160][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-01-16 10:43:47.162][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-01-16 10:43:47.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.169][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-01-16 10:43:47.172][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-01-16 10:43:47.174][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-01-16 10:43:47.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.182][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-01-16 10:43:47.183][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-01-16 10:43:47.185][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-01-16 10:43:47.213][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-01-16 10:43:47.215][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-01-16 10:43:47.216][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-01-16 10:43:47.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.221][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-01-16 10:43:47.223][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-01-16 10:43:47.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.230][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-01-16 10:43:47.232][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-01-16 10:43:47.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.238][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-01-16 10:43:47.240][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-01-16 10:43:47.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.247][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-01-16 10:43:47.250][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-01-16 10:43:47.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.256][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-01-16 10:43:47.257][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-01-16 10:43:47.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.263][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-01-16 10:43:47.264][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-01-16 10:43:47.274][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-01-16 10:43:47.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.282][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-01-16 10:43:47.284][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-01-16 10:43:47.286][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-01-16 10:43:47.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.293][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-01-16 10:43:47.297][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-01-16 10:43:47.299][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-01-16 10:43:47.301][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:47.303][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-16 10:43:47.305][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:47.307][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-16 10:43:47.309][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-16 10:43:47.311][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-16 10:43:47.313][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-01-16 10:43:47.314][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-16 10:43:47.316][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:47.318][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-01-16 10:43:47.320][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-16 10:43:47.322][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:43:47.324][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:47.326][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-01-16 10:43:47.326][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-01-16 10:43:47.326][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-01-16 10:43:47.326][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-01-16 10:43:47.326][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-01-16 10:43:47.328][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-16 10:43:47.330][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:43:47.331][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:43:47.332][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-16 10:43:47.334][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:43:47.335][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:43:47.337][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-16 10:43:47.339][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:43:47.340][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-16 10:43:47.342][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-16 10:43:47.344][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-16 10:43:47.346][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:43:47.348][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-01-16 10:43:47.352][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-01-16 10:43:47.354][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-01-16 10:43:47.356][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:47.357][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-16 10:43:47.359][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:47.361][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-16 10:43:47.363][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-16 10:43:47.365][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-16 10:43:47.366][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-01-16 10:43:47.368][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-16 10:43:47.370][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:47.372][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-01-16 10:43:47.373][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-16 10:43:47.375][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:43:47.377][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:47.379][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-01-16 10:43:47.379][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-01-16 10:43:47.379][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-01-16 10:43:47.379][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-01-16 10:43:47.379][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-01-16 10:43:47.381][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-16 10:43:47.383][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:43:47.384][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:43:47.386][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-16 10:43:47.388][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:43:47.390][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:43:47.392][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-16 10:43:47.394][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:43:47.396][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-16 10:43:47.397][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-16 10:43:47.399][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-16 10:43:47.401][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:43:47.402][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-01-16 10:43:47.405][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:47.406][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-01-16 10:43:47.408][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:47.410][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-16 10:43:47.412][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:47.414][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-16 10:43:47.415][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-16 10:43:47.416][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-16 10:43:47.418][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-01-16 10:43:47.420][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-16 10:43:47.421][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-01-16 10:43:47.423][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-01-16 10:43:47.425][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-16 10:43:47.427][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:43:47.429][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:47.431][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:43:47.433][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-16 10:43:47.435][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:43:47.437][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:43:47.438][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-16 10:43:47.440][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:43:47.442][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:43:47.444][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-16 10:43:47.446][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:43:47.448][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-16 10:43:47.449][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-16 10:43:47.450][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-16 10:43:47.452][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:43:47.454][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-01-16 10:43:47.458][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:47.460][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-01-16 10:43:47.462][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:47.464][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-16 10:43:47.466][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:47.468][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-16 10:43:47.489][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-16 10:43:47.492][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-16 10:43:47.494][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-01-16 10:43:47.496][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-16 10:43:47.498][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-01-16 10:43:47.500][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-01-16 10:43:47.502][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-16 10:43:47.504][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:43:47.506][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:47.508][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:43:47.510][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-16 10:43:47.512][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:43:47.514][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:43:47.516][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-16 10:43:47.518][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:43:47.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:43:47.522][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-16 10:43:47.524][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:43:47.526][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-16 10:43:47.528][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-16 10:43:47.530][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-16 10:43:47.532][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:43:47.535][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-01-16 10:43:47.537][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.539][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[2022-01-16 10:43:47.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.549][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[2022-01-16 10:43:47.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.574][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[2022-01-16 10:43:47.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.581][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[2022-01-16 10:43:47.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.616][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[2022-01-16 10:43:47.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.631][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[2022-01-16 10:43:47.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.679][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-01-16 10:43:47.682][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-01-16 10:43:47.685][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-01-16 10:43:47.687][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-01-16 10:43:47.690][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-01-16 10:43:47.692][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-01-16 10:43:47.695][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-01-16 10:43:47.698][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-01-16 10:43:47.701][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-01-16 10:43:47.705][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-01-16 10:43:47.709][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-01-16 10:43:47.711][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-01-16 10:43:47.714][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-01-16 10:43:47.717][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-01-16 10:43:47.720][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-01-16 10:43:47.722][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-01-16 10:43:47.724][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-01-16 10:43:47.727][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-01-16 10:43:47.730][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-01-16 10:43:47.733][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-01-16 10:43:47.735][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-01-16 10:43:47.737][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-01-16 10:43:47.739][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-01-16 10:43:47.742][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-01-16 10:43:47.745][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-01-16 10:43:47.746][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-01-16 10:43:47.765][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-01-16 10:43:47.766][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-01-16 10:43:47.768][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-01-16 10:43:47.770][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-01-16 10:43:47.773][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-01-16 10:43:47.776][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-01-16 10:43:47.778][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-01-16 10:43:47.779][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-01-16 10:43:47.781][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-01-16 10:43:47.784][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-01-16 10:43:47.785][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-01-16 10:43:47.788][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-01-16 10:43:47.791][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-01-16 10:43:47.794][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-01-16 10:43:47.797][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-01-16 10:43:47.799][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-01-16 10:43:47.801][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-01-16 10:43:47.803][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-01-16 10:43:47.806][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-01-16 10:43:47.809][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-01-16 10:43:47.811][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-01-16 10:43:47.814][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-01-16 10:43:47.817][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-01-16 10:43:47.820][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-01-16 10:43:47.823][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-01-16 10:43:47.825][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-01-16 10:43:47.826][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-01-16 10:43:47.828][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-01-16 10:43:47.830][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-01-16 10:43:47.831][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-01-16 10:43:47.833][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-01-16 10:43:47.836][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-01-16 10:43:47.838][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-01-16 10:43:47.841][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-01-16 10:43:47.844][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-01-16 10:43:47.846][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-01-16 10:43:47.849][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-01-16 10:43:47.852][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-01-16 10:43:47.854][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-01-16 10:43:47.857][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-01-16 10:43:47.860][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-01-16 10:43:47.864][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-01-16 10:43:47.866][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-01-16 10:43:47.868][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-01-16 10:43:47.871][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-01-16 10:43:47.874][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-01-16 10:43:47.877][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-01-16 10:43:47.880][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-01-16 10:43:47.883][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-01-16 10:43:47.886][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-01-16 10:43:47.889][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-01-16 10:43:47.892][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-01-16 10:43:47.895][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-01-16 10:43:47.897][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-01-16 10:43:47.899][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-01-16 10:43:47.903][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-01-16 10:43:47.906][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-01-16 10:43:47.909][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-01-16 10:43:47.910][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-01-16 10:43:47.912][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-01-16 10:43:47.913][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.915][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:47.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:47.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:47.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:47.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:47.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:47.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:47.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:47.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:47.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:47.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:47.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:47.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:47.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:47.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:47.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:47.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:47.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:47.993][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[2022-01-16 10:43:47.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:47.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:47.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:48.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:48.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:48.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:48.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:48.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:48.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:48.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:48.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:48.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:48.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:48.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:48.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:48.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:48.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:48.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:48.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:48.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:48.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:48.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:48.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:48.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:48.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:48.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:48.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:48.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:48.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:48.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:48.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:48.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:48.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:48.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:48.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:48.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:48.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:48.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:48.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:48.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:48.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:48.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:48.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:48.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:48.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:48.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:48.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:48.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:48.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:48.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:48.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:48.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:48.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:48.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:48.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:48.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:48.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:48.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:48.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:48.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:48.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:48.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:48.104][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[2022-01-16 10:43:48.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:43:48.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:43:48.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:43:48.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:43:48.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:43:48.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:43:48.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:43:48.116][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-01-16 10:43:48.118][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-01-16 10:43:48.121][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-01-16 10:43:48.122][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-01-16 10:43:48.124][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:48.125][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-16 10:43:48.127][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:48.129][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-16 10:43:48.131][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:48.133][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-16 10:43:48.134][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-01-16 10:43:48.135][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-16 10:43:48.137][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:48.139][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-01-16 10:43:48.141][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-16 10:43:48.143][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-01-16 10:43:48.143][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-01-16 10:43:48.143][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-01-16 10:43:48.143][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-01-16 10:43:48.143][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-01-16 10:43:48.143][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-01-16 10:43:48.143][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-01-16 10:43:48.143][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-01-16 10:43:48.143][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-01-16 10:43:48.145][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-01-16 10:43:48.147][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-01-16 10:43:48.147][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-01-16 10:43:48.149][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-16 10:43:48.151][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:43:48.153][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:43:48.155][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-16 10:43:48.156][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:43:48.157][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:43:48.158][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-16 10:43:48.160][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-01-16 10:43:48.160][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-01-16 10:43:48.162][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-16 10:43:48.164][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-16 10:43:48.166][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-01-16 10:43:48.168][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:43:48.170][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-01-16 10:43:48.172][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-01-16 10:43:48.176][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-01-16 10:43:48.178][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-01-16 10:43:48.180][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-01-16 10:43:48.182][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-01-16 10:43:48.184][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-01-16 10:43:48.185][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-01-16 10:43:48.187][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-01-16 10:43:48.189][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-01-16 10:43:48.191][biodb::testThat] 
biodb.INFO [2022-01-16 10:43:48.193][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2022-01-16 10:43:48.195][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:43:48.197][biodb::testThat] 
biodb.DEBUG[2022-01-16 10:43:48.240][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[2022-01-16 10:43:48.267][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:48.269][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:48.271][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2022-01-16 10:43:48.935][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2022-01-16 10:43:49.619][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-16 10:43:49.631][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2022-01-16 10:43:49.655][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2022-01-16 10:43:49.704][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2022-01-16 10:43:49.708][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:49.709][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:49.711][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2022-01-16 10:43:50.395][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[2022-01-16 10:43:51.085][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-16 10:43:51.096][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2022-01-16 10:43:51.120][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2022-01-16 10:43:51.138][biodb::testThat] 
biodb.INFO [2022-01-16 10:43:51.140][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2022-01-16 10:43:51.142][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:43:51.144][biodb::testThat] 
biodb.INFO [2022-01-16 10:43:51.163][biodb::testThat] 
biodb.INFO [2022-01-16 10:43:51.164][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2022-01-16 10:43:51.166][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:43:51.168][biodb::testThat] 
biodb.DEBUG[2022-01-16 10:43:51.256][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[2022-01-16 10:43:51.259][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:51.261][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:51.262][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2022-01-16 10:43:51.741][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2022-01-16 10:43:52.262][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-16 10:43:52.278][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2022-01-16 10:43:52.303][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2022-01-16 10:43:52.360][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2022-01-16 10:43:52.366][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-01-16 10:43:52.369][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2022-01-16 10:43:52.372][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-01-16 10:43:52.374][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2022-01-16 10:43:52.455][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2022-01-16 10:43:52.461][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:52.463][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:52.466][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2022-01-16 10:43:52.964][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[2022-01-16 10:43:53.484][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-16 10:43:53.501][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2022-01-16 10:43:53.526][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2022-01-16 10:43:53.601][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[2022-01-16 10:43:53.606][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:53.608][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:53.610][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2022-01-16 10:43:55.012][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2022-01-16 10:43:56.846][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-16 10:43:56.865][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2022-01-16 10:43:56.905][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2022-01-16 10:43:57.055][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2022-01-16 10:43:57.060][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:43:57.063][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:43:57.065][private$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[2022-01-16 10:43:58.375][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[2022-01-16 10:44:00.108][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-01-16 10:44:00.126][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2022-01-16 10:44:00.163][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2022-01-16 10:44:00.242][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-01-16 10:44:00.244][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-01-16 10:44:00.246][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-01-16 10:44:00.248][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-01-16 10:44:00.249][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:00.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:00.252][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:00.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:00.255][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.257][FUN] Functions in observer BiodbConfig: [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 [2022-01-16 10:44:00.264][biodb::testContext] 
biodb.INFO [2022-01-16 10:44:00.265][biodb::testContext] ********************************************************************************
biodb.INFO [2022-01-16 10:44:00.266][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2022-01-16 10:44:00.268][biodb::testContext] ********************************************************************************
biodb.INFO [2022-01-16 10:44:00.269][biodb::testContext] 
biodb.INFO [2022-01-16 10:44:00.277][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-01-16 10:44:00.279][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-01-16 10:44:00.284][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-01-16 10:44:00.285][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-01-16 10:44:00.286][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-01-16 10:44:00.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.291][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-01-16 10:44:00.292][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-01-16 10:44:00.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.317][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-01-16 10:44:00.318][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-01-16 10:44:00.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.323][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-01-16 10:44:00.324][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-01-16 10:44:00.325][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-01-16 10:44:00.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.329][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-01-16 10:44:00.331][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-01-16 10:44:00.332][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-01-16 10:44:00.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.339][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-01-16 10:44:00.341][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-01-16 10:44:00.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.346][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-01-16 10:44:00.347][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-01-16 10:44:00.348][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-01-16 10:44:00.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.352][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-01-16 10:44:00.353][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-01-16 10:44:00.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.357][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-01-16 10:44:00.359][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-01-16 10:44:00.360][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-01-16 10:44:00.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.366][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-01-16 10:44:00.368][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-01-16 10:44:00.370][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-01-16 10:44:00.372][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-01-16 10:44:00.374][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-01-16 10:44:00.376][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-01-16 10:44:00.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.382][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-01-16 10:44:00.384][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-01-16 10:44:00.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.391][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-01-16 10:44:00.393][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-01-16 10:44:00.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.399][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-01-16 10:44:00.401][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-01-16 10:44:00.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.405][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-01-16 10:44:00.407][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-01-16 10:44:00.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.411][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[2022-01-16 10:44:00.413][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-01-16 10:44:00.415][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-01-16 10:44:00.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.421][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-01-16 10:44:00.423][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-01-16 10:44:00.434][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-01-16 10:44:00.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.441][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-01-16 10:44:00.443][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-01-16 10:44:00.445][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-01-16 10:44:00.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.452][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-01-16 10:44:00.455][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-01-16 10:44:00.456][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-01-16 10:44:00.458][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:00.460][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-16 10:44:00.462][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:00.463][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-16 10:44:00.465][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-16 10:44:00.467][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-16 10:44:00.469][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-01-16 10:44:00.470][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-16 10:44:00.471][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:00.472][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-01-16 10:44:00.473][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-16 10:44:00.475][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:44:00.476][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:00.477][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-01-16 10:44:00.477][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-01-16 10:44:00.477][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-01-16 10:44:00.477][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-01-16 10:44:00.477][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-01-16 10:44:00.478][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-16 10:44:00.480][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:44:00.481][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:44:00.482][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-16 10:44:00.483][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:44:00.484][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:44:00.485][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-16 10:44:00.486][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:44:00.487][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-16 10:44:00.488][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-16 10:44:00.490][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-16 10:44:00.492][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:44:00.495][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-01-16 10:44:00.498][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-01-16 10:44:00.500][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-01-16 10:44:00.502][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:00.504][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-16 10:44:00.506][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:00.508][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-16 10:44:00.510][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-16 10:44:00.512][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-16 10:44:00.514][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-01-16 10:44:00.515][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-16 10:44:00.518][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:00.519][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-01-16 10:44:00.520][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-16 10:44:00.522][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:44:00.524][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:00.526][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-01-16 10:44:00.526][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-01-16 10:44:00.526][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-01-16 10:44:00.526][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-01-16 10:44:00.526][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-01-16 10:44:00.528][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-16 10:44:00.530][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:44:00.532][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:44:00.533][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-16 10:44:00.535][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:44:00.537][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:44:00.539][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-16 10:44:00.541][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:44:00.542][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-16 10:44:00.560][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-16 10:44:00.562][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-16 10:44:00.565][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:44:00.567][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-01-16 10:44:00.571][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:00.573][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-01-16 10:44:00.575][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:00.577][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-16 10:44:00.579][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:00.581][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-16 10:44:00.583][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-16 10:44:00.585][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-16 10:44:00.587][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-01-16 10:44:00.589][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-16 10:44:00.591][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-01-16 10:44:00.593][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-01-16 10:44:00.595][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-16 10:44:00.596][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:44:00.597][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:00.598][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:44:00.600][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-16 10:44:00.602][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:44:00.604][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:44:00.607][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-16 10:44:00.609][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:44:00.611][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:44:00.613][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-16 10:44:00.615][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:44:00.617][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-16 10:44:00.619][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-16 10:44:00.620][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-16 10:44:00.622][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:44:00.623][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-01-16 10:44:00.625][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:00.626][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-01-16 10:44:00.628][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:00.630][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-16 10:44:00.632][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:00.634][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-16 10:44:00.635][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-01-16 10:44:00.636][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-16 10:44:00.637][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-01-16 10:44:00.638][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-16 10:44:00.640][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-01-16 10:44:00.641][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-01-16 10:44:00.642][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-16 10:44:00.644][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:44:00.850][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:00.852][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:44:00.854][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-16 10:44:00.856][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:44:00.858][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:44:00.860][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-16 10:44:00.862][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:44:00.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:44:00.866][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-16 10:44:00.868][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:44:00.870][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-16 10:44:00.872][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-16 10:44:00.874][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-01-16 10:44:00.876][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:44:00.879][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-01-16 10:44:00.881][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:00.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:00.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:00.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:00.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.896][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[2022-01-16 10:44:00.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:00.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:00.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:00.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:00.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:00.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:00.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:00.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:00.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:00.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:00.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:00.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:00.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:00.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:00.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.944][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[2022-01-16 10:44:00.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:00.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:00.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:00.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:00.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:00.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:00.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:00.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:00.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:00.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:00.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:00.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:00.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:00.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:00.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:00.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:00.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:00.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:01.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.032][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-01-16 10:44:01.035][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-01-16 10:44:01.039][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-01-16 10:44:01.042][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-01-16 10:44:01.045][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-01-16 10:44:01.046][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-01-16 10:44:01.048][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-01-16 10:44:01.050][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-01-16 10:44:01.051][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-01-16 10:44:01.053][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-01-16 10:44:01.055][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-01-16 10:44:01.056][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-01-16 10:44:01.058][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-01-16 10:44:01.059][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-01-16 10:44:01.061][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-01-16 10:44:01.063][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-01-16 10:44:01.064][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-01-16 10:44:01.066][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-01-16 10:44:01.067][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-01-16 10:44:01.069][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-01-16 10:44:01.071][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-01-16 10:44:01.072][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-01-16 10:44:01.074][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-01-16 10:44:01.076][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-01-16 10:44:01.077][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-01-16 10:44:01.079][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-01-16 10:44:01.080][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-01-16 10:44:01.082][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-01-16 10:44:01.084][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-01-16 10:44:01.087][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-01-16 10:44:01.090][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-01-16 10:44:01.093][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-01-16 10:44:01.095][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-01-16 10:44:01.098][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-01-16 10:44:01.100][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-01-16 10:44:01.103][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-01-16 10:44:01.105][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-01-16 10:44:01.107][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-01-16 10:44:01.109][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-01-16 10:44:01.110][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-01-16 10:44:01.112][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-01-16 10:44:01.114][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-01-16 10:44:01.116][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-01-16 10:44:01.118][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-01-16 10:44:01.121][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-01-16 10:44:01.124][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-01-16 10:44:01.127][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-01-16 10:44:01.129][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-01-16 10:44:01.131][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-01-16 10:44:01.133][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-01-16 10:44:01.135][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-01-16 10:44:01.136][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-01-16 10:44:01.139][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-01-16 10:44:01.142][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-01-16 10:44:01.145][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-01-16 10:44:01.148][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-01-16 10:44:01.150][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-01-16 10:44:01.153][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-01-16 10:44:01.154][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-01-16 10:44:01.156][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-01-16 10:44:01.159][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-01-16 10:44:01.161][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-01-16 10:44:01.164][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-01-16 10:44:01.167][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-01-16 10:44:01.169][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-01-16 10:44:01.170][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-01-16 10:44:01.172][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-01-16 10:44:01.174][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-01-16 10:44:01.177][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-01-16 10:44:01.179][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-01-16 10:44:01.181][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-01-16 10:44:01.184][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-01-16 10:44:01.187][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-01-16 10:44:01.190][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-01-16 10:44:01.193][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-01-16 10:44:01.196][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-01-16 10:44:01.199][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-01-16 10:44:01.202][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-01-16 10:44:01.205][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-01-16 10:44:01.208][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-01-16 10:44:01.211][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-01-16 10:44:01.213][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-01-16 10:44:01.216][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-01-16 10:44:01.219][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-01-16 10:44:01.221][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-01-16 10:44:01.222][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-01-16 10:44:01.223][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.225][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:01.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:01.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:01.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:01.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:01.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:01.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:01.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:01.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:01.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:01.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:01.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:01.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.271][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.DEBUG[2022-01-16 10:44:01.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:01.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:01.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:01.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:01.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:01.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:01.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:01.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:01.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:01.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:01.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:01.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:01.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:01.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:01.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:01.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:01.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:01.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:01.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:01.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:01.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:01.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:01.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:01.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:01.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:01.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:01.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:01.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:01.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:01.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:01.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:01.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:01.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:01.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:01.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:01.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:01.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-01-16 10:44:01.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:01.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:01.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:01.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:01.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:01.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:01.403][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-01-16 10:44:01.406][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-01-16 10:44:01.410][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-01-16 10:44:01.412][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-01-16 10:44:01.414][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:01.416][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-01-16 10:44:01.418][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:01.419][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-01-16 10:44:01.421][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:01.423][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-01-16 10:44:01.425][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-01-16 10:44:01.426][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-01-16 10:44:01.428][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:01.430][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-01-16 10:44:01.432][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-01-16 10:44:01.434][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-01-16 10:44:01.434][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-01-16 10:44:01.434][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-01-16 10:44:01.434][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-01-16 10:44:01.434][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-01-16 10:44:01.434][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-01-16 10:44:01.434][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-01-16 10:44:01.434][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-01-16 10:44:01.434][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-01-16 10:44:01.436][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-01-16 10:44:01.438][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-01-16 10:44:01.438][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-01-16 10:44:01.440][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-01-16 10:44:01.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:44:01.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:44:01.444][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-01-16 10:44:01.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-01-16 10:44:01.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-01-16 10:44:01.448][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-01-16 10:44:01.449][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-01-16 10:44:01.449][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-01-16 10:44:01.450][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-01-16 10:44:01.451][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-01-16 10:44:01.452][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-01-16 10:44:01.454][self$setPropertyValue] 
biodb.DEBUG[2022-01-16 10:44:01.457][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-01-16 10:44:01.460][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-01-16 10:44:01.466][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-01-16 10:44:01.468][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-01-16 10:44:01.484][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-01-16 10:44:01.487][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-01-16 10:44:01.490][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-01-16 10:44:01.492][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-01-16 10:44:01.494][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-01-16 10:44:01.495][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-01-16 10:44:01.497][biodb::testThat] 
biodb.INFO [2022-01-16 10:44:01.498][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2022-01-16 10:44:01.499][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-01-16 10:44:01.500][biodb::testThat] 
biodb.DEBUG[2022-01-16 10:44:01.533][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[2022-01-16 10:44:01.540][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-01-16 10:44:01.543][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2022-01-16 10:44:01.545][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-01-16 10:44:01.599][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2022-01-16 10:44:02.920][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2022-01-16 10:44:02.922][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-01-16 10:44:02.925][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2022-01-16 10:44:02.927][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2022-01-16 10:44:02.929][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-01-16 10:44:02.931][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-01-16 10:44:02.933][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-01-16 10:44:02.935][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-01-16 10:44:02.937][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-01-16 10:44:02.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:44:02.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:02.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:02.950][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:02.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:02.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:02.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:02.957][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2022-01-16 10:44:02.963][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:44:02.965][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:44:02.967][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2022-01-16 10:44:03.640][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.DEBUG[2022-01-16 10:44:04.389][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-01-16 10:44:04.408][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.content"
biodb.TRACE[2022-01-16 10:44:04.437][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.request"
biodb.DEBUG[2022-01-16 10:44:04.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:44:04.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:04.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:04.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:04.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:04.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:04.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-01-16 10:44:04.463][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2022-01-16 10:44:04.469][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-01-16 10:44:04.471][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-01-16 10:44:04.473][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2022-01-16 10:44:05.147][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2022-01-16 10:44:05.801][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-01-16 10:44:05.820][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2022-01-16 10:44:05.890][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.TRACE[2022-01-16 10:44:05.961][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv"
biodb.DEBUG[2022-01-16 10:44:05.974][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-01-16 10:44:05.994][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-01-16 10:44:05.996][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-01-16 10:44:06.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:44:06.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:06.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:06.007][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:06.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:06.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:06.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-16 10:44:06.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:06.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:06.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:06.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:06.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-16 10:44:06.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-16 10:44:06.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.061][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-01-16 10:44:06.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-01-16 10:44:06.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.070][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-01-16 10:44:06.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-01-16 10:44:06.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.085][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:06.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:06.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.096][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:06.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:06.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.116][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:06.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:06.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.126][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:06.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:06.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.143][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-16 10:44:06.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:06.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.152][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-16 10:44:06.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:06.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.170][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:44:06.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:44:06.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.180][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:44:06.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:44:06.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.203][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:06.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.213][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:06.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.232][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-16 10:44:06.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.240][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-01-16 10:44:06.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.275][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:06.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.284][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:06.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.297][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-16 10:44:06.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.317][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:06.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.326][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:06.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.337][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:06.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.347][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:06.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.357][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:06.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.375][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:06.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:06.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.386][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:06.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:06.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:06.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:06.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.406][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:06.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:06.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:06.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:06.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:06.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:06.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:06.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:06.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-16 10:44:06.453][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:44:06.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:06.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:06.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:06.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:06.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:06.466][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.TRACE[2022-01-16 10:44:06.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:06.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:06.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:06.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:06.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-16 10:44:06.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-16 10:44:06.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-16 10:44:06.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-16 10:44:06.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.537][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-01-16 10:44:06.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-01-16 10:44:06.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.548][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-01-16 10:44:06.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-01-16 10:44:06.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.558][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:06.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:06.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.567][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:06.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:06.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.585][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:06.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:06.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.596][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:06.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:06.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.643][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-16 10:44:06.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:06.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.653][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-01-16 10:44:06.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:06.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.673][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:44:06.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:44:06.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.686][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:44:06.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:44:06.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.705][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:06.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.715][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:06.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.734][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-16 10:44:06.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.744][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-01-16 10:44:06.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.755][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:06.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.765][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:06.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.776][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-01-16 10:44:06.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:06.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.794][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:06.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:06.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.804][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:06.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:06.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:06.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:06.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.822][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:06.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:06.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:06.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:06.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:06.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:06.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:06.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:06.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:06.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:06.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:06.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:06.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:06.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:06.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:06.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:06.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:06.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:06.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:06.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:06.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-01-16 10:44:06.936][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2022-01-16 10:44:06.940][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2022-01-16 10:44:06.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:44:06.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:06.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:06.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:06.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:06.955][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:06.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-01-16 10:44:06.985][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-16 10:44:06.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-16 10:44:06.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:06.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:06.994][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-16 10:44:06.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-16 10:44:07.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.006][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-01-16 10:44:07.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-01-16 10:44:07.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.015][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-01-16 10:44:07.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-01-16 10:44:07.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.024][private$selectFields] Fields none
biodb.TRACE[2022-01-16 10:44:07.026][private$selectFields] 
biodb.TRACE[2022-01-16 10:44:07.029][private$selectFields] Fields is null: TRUE
biodb.TRACE[2022-01-16 10:44:07.030][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-16 10:44:07.034][private$selectFields] Fields [7]: "accession, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:44:07.036][ef$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:07.038][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:07.040][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.043][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.047][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.050][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.052][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.054][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.057][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.060][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.062][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.064][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.067][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:07.070][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:07.072][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.074][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.076][ef$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:44:07.080][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:44:07.082][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.084][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.086][ef$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:07.089][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:07.091][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.093][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.096][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:07.098][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:07.100][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.102][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.104][ef$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:07.106][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:07.108][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.110][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.113][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.115][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.117][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.120][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.123][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.126][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.129][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.131][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.133][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:07.137][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:07.139][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.140][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.142][ef$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:44:07.146][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:44:07.148][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.150][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.153][ef$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:07.155][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:07.162][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.164][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.167][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:07.170][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:07.174][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.176][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.179][private$selectFields] Fields [7]: "accession, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:44:07.181][private$organizeFieldsByGroups] Fields [7]: "accession, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:44:07.184][ef$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:07.187][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:07.189][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.191][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.193][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.196][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.199][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.201][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.203][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.208][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.210][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.212][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.214][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:07.217][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:07.219][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.221][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.223][ef$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:44:07.225][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:44:07.227][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.230][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.232][ef$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:07.234][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:07.236][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.238][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.240][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:07.242][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:07.245][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.247][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.249][private$organizeFieldsByGroups] Groups [2]: "c("accession", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2022-01-16 10:44:07.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:07.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:07.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:07.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:07.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:07.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:07.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.280][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.289][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.301][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.312][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.350][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.360][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:07.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:07.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:07.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:07.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:07.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:07.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.404][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:44:07.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:44:07.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.414][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:44:07.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:44:07.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.422][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:44:07.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:44:07.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.435][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:07.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:07.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.444][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:07.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:07.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.453][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:07.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:07.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.464][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:07.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:07.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.481][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:07.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:07.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.493][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:07.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:07.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.526][private$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[2022-01-16 10:44:07.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-01-16 10:44:07.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:07.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:07.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:07.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:07.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:07.549][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.TRACE[2022-01-16 10:44:07.553][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-16 10:44:07.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-16 10:44:07.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.565][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-01-16 10:44:07.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-01-16 10:44:07.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.575][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-01-16 10:44:07.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-01-16 10:44:07.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.584][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-01-16 10:44:07.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-01-16 10:44:07.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.595][private$selectFields] Fields none
biodb.TRACE[2022-01-16 10:44:07.598][private$selectFields] 
biodb.TRACE[2022-01-16 10:44:07.600][private$selectFields] Fields is null: TRUE
biodb.TRACE[2022-01-16 10:44:07.602][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-01-16 10:44:07.606][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:44:07.609][ef$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:07.611][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:07.613][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.615][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.618][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-16 10:44:07.621][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-16 10:44:07.623][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.625][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.628][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.630][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.632][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.634][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.636][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.639][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.641][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.643][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.646][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:07.648][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:07.652][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.654][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.656][ef$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:44:07.659][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:44:07.662][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.664][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.667][ef$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:07.669][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:07.671][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.675][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.677][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:07.679][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:07.681][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.685][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.688][ef$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:07.690][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:07.692][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.694][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.699][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-16 10:44:07.701][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-16 10:44:07.703][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.705][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.707][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.711][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.713][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.741][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.744][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.747][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.749][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.752][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.756][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:07.758][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:07.760][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.762][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.765][ef$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:44:07.770][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:44:07.772][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.774][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.776][ef$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:07.778][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:07.787][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.789][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.792][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:07.794][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:07.796][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.799][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.801][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:44:07.803][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-01-16 10:44:07.806][ef$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:07.811][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:07.813][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.815][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.817][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-16 10:44:07.820][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-16 10:44:07.823][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.825][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.827][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.829][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.836][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.838][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.840][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.842][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.844][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.848][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.851][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:07.853][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:07.856][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.858][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.862][ef$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:44:07.864][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:44:07.866][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.868][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.872][ef$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:07.874][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:07.876][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.878][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.880][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:07.884][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:07.886][ef$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.888][ef$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.890][private$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[2022-01-16 10:44:07.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:07.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:07.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:07.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:07.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-01-16 10:44:07.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-01-16 10:44:07.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-16 10:44:07.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-16 10:44:07.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-16 10:44:07.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-16 10:44:07.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-01-16 10:44:07.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-01-16 10:44:07.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.958][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.966][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.978][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-01-16 10:44:07.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.989][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:07.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:07.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:07.998][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:08.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:08.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:08.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:08.007][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:08.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-01-16 10:44:08.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:08.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:08.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:08.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:08.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:08.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:08.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:08.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:08.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:08.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:08.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:08.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-01-16 10:44:08.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:08.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:08.043][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:44:08.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:44:08.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:08.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:08.055][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:44:08.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:44:08.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:08.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:08.067][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-01-16 10:44:08.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-01-16 10:44:08.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:08.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:08.076][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:08.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:08.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:08.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:08.089][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:08.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:08.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:08.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:08.127][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-01-16 10:44:08.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-01-16 10:44:08.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:08.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:08.139][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:08.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:08.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:08.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:08.152][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:08.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:08.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:08.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:08.162][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:08.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-01-16 10:44:08.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-01-16 10:44:08.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-01-16 10:44:08.181][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2022-01-16 10:44:08.183][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2022-01-16 10:44:08.185][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2022-01-16 10:44:08.193][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-01-16 10:44:08.196][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-01-16 10:44:08.199][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-01-16 10:44:08.201][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-01-16 10:44:08.203][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-01-16 10:44:08.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-01-16 10:44:08.207][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-01-16 10:44:08.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-01-16 10:44:08.211][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-01-16 10:44:08.213][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 170 ]
> 
> proc.time()
   user  system elapsed 
 34.058   2.196 128.984 

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn3.3510.6354.007
LipidmapsStructureEntry0.6190.0110.629