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This page was generated on 2022-04-13 12:07:41 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for biodbLipidmaps on machv2


To the developers/maintainers of the biodbLipidmaps package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbLipidmaps.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 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 -0400 (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: 2022-04-12 10:52:16 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 10:56:03 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 226.9 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 4.1.3 (2022-03-10)
* 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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2022-04-12 10:53:24.901][biodb::testContext] 
biodb.INFO [2022-04-12 10:53:24.917][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:53:24.918][biodb::testContext] Test context - Generic tests
biodb.INFO [2022-04-12 10:53:24.920][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:53:24.921][biodb::testContext] 
biodb.INFO [2022-04-12 10:53:24.967][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:53:24.970][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-04-12 10:53:24.986][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:53:24.989][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-04-12 10:53:24.991][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-04-12 10:53:24.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:24.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:24.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.000][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-04-12 10:53:25.047][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-04-12 10:53:25.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.055][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-04-12 10:53:25.058][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-04-12 10:53:25.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.066][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-04-12 10:53:25.069][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-04-12 10:53:25.072][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-04-12 10:53:25.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.080][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-04-12 10:53:25.083][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-04-12 10:53:25.085][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-04-12 10:53:25.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.093][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-04-12 10:53:25.096][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-04-12 10:53:25.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.104][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-04-12 10:53:25.107][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-04-12 10:53:25.109][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-04-12 10:53:25.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.119][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-04-12 10:53:25.121][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-04-12 10:53:25.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.127][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-04-12 10:53:25.129][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-04-12 10:53:25.132][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-04-12 10:53:25.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.140][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:53:25.142][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-04-12 10:53:25.143][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-04-12 10:53:25.145][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-04-12 10:53:25.146][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-04-12 10:53:25.148][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-04-12 10:53:25.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.155][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-04-12 10:53:25.158][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-04-12 10:53:25.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.166][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-04-12 10:53:25.168][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-04-12 10:53:25.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.173][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[2022-04-12 10:53:25.174][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-04-12 10:53:25.176][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-04-12 10:53:25.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.186][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-04-12 10:53:25.188][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-04-12 10:53:25.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.197][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-04-12 10:53:25.199][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-04-12 10:53:25.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.208][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:53:25.210][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-04-12 10:53:25.222][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-04-12 10:53:25.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.229][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-04-12 10:53:25.232][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-04-12 10:53:25.234][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-04-12 10:53:25.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.248][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-04-12 10:53:25.329][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:25.369][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-04-12 10:53:25.372][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:25.374][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:25.376][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:25.379][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:25.381][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:25.383][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:25.385][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:53:25.387][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:25.389][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:25.390][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-04-12 10:53:25.392][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:25.393][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:53:25.405][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:25.407][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:53:25.407][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:53:25.407][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:53:25.407][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:53:25.407][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:53:25.409][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:25.411][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:25.412][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:25.415][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:25.417][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:25.418][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:25.420][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:25.422][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:53:25.424][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:25.426][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:25.428][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:25.430][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:53:25.433][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-04-12 10:53:25.436][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:25.438][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:53:25.440][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:25.442][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:25.444][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:25.446][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:25.448][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:25.450][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:25.451][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:53:25.452][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:25.454][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:25.456][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-04-12 10:53:25.458][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:25.460][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:53:25.461][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:25.462][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:53:25.462][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:53:25.462][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:53:25.462][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:53:25.462][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:53:25.464][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:25.466][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:25.468][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:25.470][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:25.471][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:25.473][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:25.475][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:25.476][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:53:25.478][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:25.479][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:25.480][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:25.481][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:53:25.483][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-04-12 10:53:25.487][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:25.489][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-04-12 10:53:25.491][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:25.493][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:25.495][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:25.496][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:25.498][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:25.500][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:25.502][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:53:25.504][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:25.505][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:25.507][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-04-12 10:53:25.509][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:25.511][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:53:25.512][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:25.515][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:53:25.517][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:25.519][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:25.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:25.522][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:25.524][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:25.525][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:25.527][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:25.529][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:53:25.531][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:25.532][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:25.534][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:25.536][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:53:25.539][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-04-12 10:53:25.542][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:25.544][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:53:25.546][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:25.548][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:25.550][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:25.551][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:25.552][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:25.554][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:25.555][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:53:25.557][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:25.559][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:25.561][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-04-12 10:53:25.563][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:25.564][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:53:25.566][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:25.568][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:53:25.570][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:25.572][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:25.574][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:25.576][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:25.577][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:25.578][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:25.579][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:25.581][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:53:25.583][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:25.584][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:25.586][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:25.588][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:53:25.596][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:53:25.598][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.641][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[2022-04-12 10:53:25.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.705][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[2022-04-12 10:53:25.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:25.713][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-04-12 10:53:25.723][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-04-12 10:53:25.726][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-04-12 10:53:25.729][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-04-12 10:53:25.732][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 10:53:25.734][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-04-12 10:53:25.737][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-04-12 10:53:25.739][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-04-12 10:53:25.742][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-04-12 10:53:25.745][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-04-12 10:53:25.747][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 10:53:25.749][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-04-12 10:53:25.752][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-04-12 10:53:25.755][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-04-12 10:53:25.758][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-04-12 10:53:25.762][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 10:53:25.765][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-04-12 10:53:25.768][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-04-12 10:53:25.771][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 10:53:25.774][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-04-12 10:53:25.777][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-04-12 10:53:25.780][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-04-12 10:53:25.783][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-04-12 10:53:25.786][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-04-12 10:53:25.789][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-04-12 10:53:25.792][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-04-12 10:53:25.796][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-04-12 10:53:25.799][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-04-12 10:53:25.802][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-04-12 10:53:25.805][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-04-12 10:53:25.808][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-04-12 10:53:25.811][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-04-12 10:53:25.814][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-04-12 10:53:25.817][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-04-12 10:53:25.820][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-04-12 10:53:25.823][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-04-12 10:53:25.826][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-04-12 10:53:25.829][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-04-12 10:53:25.833][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-04-12 10:53:25.836][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-04-12 10:53:25.839][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-04-12 10:53:25.842][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-04-12 10:53:25.845][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-04-12 10:53:25.848][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-04-12 10:53:25.851][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-04-12 10:53:25.854][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-04-12 10:53:25.856][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-04-12 10:53:25.860][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-04-12 10:53:25.871][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-04-12 10:53:25.874][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-04-12 10:53:25.877][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-04-12 10:53:25.879][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-04-12 10:53:25.881][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-04-12 10:53:25.884][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-04-12 10:53:25.887][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-04-12 10:53:25.890][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-04-12 10:53:25.893][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-04-12 10:53:25.896][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-04-12 10:53:25.899][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-04-12 10:53:25.902][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-04-12 10:53:25.904][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-04-12 10:53:25.906][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-04-12 10:53:25.908][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-04-12 10:53:25.910][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-04-12 10:53:25.913][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-04-12 10:53:25.916][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-04-12 10:53:25.919][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 10:53:25.922][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 10:53:25.925][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-04-12 10:53:25.928][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-04-12 10:53:25.931][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-04-12 10:53:25.934][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-04-12 10:53:25.936][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-04-12 10:53:25.938][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-04-12 10:53:25.941][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-04-12 10:53:25.943][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-04-12 10:53:25.946][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-04-12 10:53:25.948][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-04-12 10:53:25.951][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-04-12 10:53:25.953][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-04-12 10:53:25.955][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-04-12 10:53:25.958][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-04-12 10:53:25.960][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-04-12 10:53:25.971][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-04-12 10:53:25.974][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:53:25.980][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:53:25.981][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.984][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.986][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[2022-04-12 10:53:25.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:25.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:26.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:26.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:26.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:26.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:26.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:26.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:26.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:26.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:26.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:26.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:26.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:26.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:26.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:26.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:26.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:26.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:26.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:26.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:26.030][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[2022-04-12 10:53:26.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:26.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:26.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:26.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:26.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:26.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:26.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:26.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:26.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:26.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:26.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:26.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:26.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:26.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:26.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:26.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:26.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:26.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:26.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:26.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:26.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:26.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:26.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:26.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:26.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:26.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:26.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:26.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:26.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:26.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:26.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:26.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:26.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:26.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:26.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:26.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:26.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:26.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:26.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:26.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:26.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:26.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:26.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:26.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:26.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:26.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:26.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:26.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:26.108][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[2022-04-12 10:53:26.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:26.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:26.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:26.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:26.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:26.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:26.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:26.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:26.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:26.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:26.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:26.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:26.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:26.130][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[2022-04-12 10:53:26.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:26.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:26.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:26.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:26.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:26.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:26.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:26.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:26.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:26.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:26.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:26.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:26.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:26.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:26.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:26.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:26.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:26.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:26.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:26.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:26.168][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[2022-04-12 10:53:26.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:26.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:26.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:26.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:26.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:26.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:26.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:26.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:26.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:26.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:26.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:26.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:26.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:26.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:26.192][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-04-12 10:53:26.213][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-04-12 10:53:26.216][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:26.218][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-04-12 10:53:26.220][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:26.223][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:26.225][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:26.227][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:26.229][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:26.231][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:26.232][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:53:26.233][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:26.234][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:26.235][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-04-12 10:53:26.237][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:26.238][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-04-12 10:53:26.238][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-04-12 10:53:26.238][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-04-12 10:53:26.238][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-04-12 10:53:26.238][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-04-12 10:53:26.238][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-04-12 10:53:26.238][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-04-12 10:53:26.238][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-04-12 10:53:26.238][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-04-12 10:53:26.239][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:26.240][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:53:26.240][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:53:26.242][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:26.243][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:26.244][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:26.246][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:26.248][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:26.249][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:26.251][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:26.253][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-04-12 10:53:26.253][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-04-12 10:53:26.255][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:26.257][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:26.259][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:26.261][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:53:26.273][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-04-12 10:53:26.276][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 10:53:26.319][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-04-12 10:53:26.321][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-04-12 10:53:26.329][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-04-12 10:53:26.336][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-04-12 10:53:26.345][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-04-12 10:53:26.358][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-04-12 10:53:26.360][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-04-12 10:53:26.363][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-04-12 10:53:26.431][biodb::testThat] 
biodb.INFO [2022-04-12 10:53:26.433][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2022-04-12 10:53:26.434][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:26.436][biodb::testThat] 
biodb.TRACE[2022-04-12 10:53:26.443][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[2022-04-12 10:53:26.458][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:26.463][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-04-12 10:53:26.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:26.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:26.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:26.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:26.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:26.484][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:26.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:26.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:26.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:26.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:26.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:26.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:26.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:26.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.556][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:26.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:26.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.564][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:26.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:26.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.572][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:26.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:26.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.629][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:26.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:26.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.656][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:26.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:26.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.664][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:26.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:26.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.688][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-04-12 10:53:26.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:26.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.697][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-04-12 10:53:26.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:26.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.725][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:26.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:26.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.733][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:26.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:26.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:26.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:26.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.770][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:26.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:26.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.805][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-04-12 10:53:26.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:26.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.810][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-04-12 10:53:26.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:26.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.818][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:26.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:26.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.826][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:26.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:26.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.835][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-04-12 10:53:26.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:26.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.894][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:26.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:26.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.900][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:26.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:26.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.985][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:26.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:26.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:26.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:26.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:26.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:26.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.002][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:27.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:27.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.030][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:27.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:27.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.037][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:27.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:27.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.052][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:27.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:27.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:27.125][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2022-04-12 10:53:27.146][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:53:27.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:53:27.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.154][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:53:27.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:53:27.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.162][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-04-12 10:53:27.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-04-12 10:53:27.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.170][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-04-12 10:53:27.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-04-12 10:53:27.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.251][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:27.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:27.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.302][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:27.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:27.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.310][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:27.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:27.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.318][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:27.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:27.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.362][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.364][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.366][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.367][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.390][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:27.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:27.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:27.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:27.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.405][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:27.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:27.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.412][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:27.415][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:27.417][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.419][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.421][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:27.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:27.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.441][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:27.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:27.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.450][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:27.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:27.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.459][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:27.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:27.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.468][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:27.470][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:27.472][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.474][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.476][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:27.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:27.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.496][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:27.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:27.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.501][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:27.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:27.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.506][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:27.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:27.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.511][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:27.513][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:27.515][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.517][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.519][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:27.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:27.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:27.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:27.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:27.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:27.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:27.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:27.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.565][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:27.567][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:27.569][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.571][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:27.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:27.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.595][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:27.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:27.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.603][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:27.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:27.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.611][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:27.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:27.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.620][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:27.622][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:27.623][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.625][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.627][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:27.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:27.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.672][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.674][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.676][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.678][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.688][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:27.690][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:27.692][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.694][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.702][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:27.705][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:27.707][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.708][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.718][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:27.720][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:27.722][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.723][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.733][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:27.735][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:27.737][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.739][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.749][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:27.751][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:27.753][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.755][ef$get] fields variable is a list.
biodb.INFO [2022-04-12 10:53:27.766][biodb::testThat] 
biodb.INFO [2022-04-12 10:53:27.768][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2022-04-12 10:53:27.770][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:27.771][biodb::testThat] 
biodb.DEBUG[2022-04-12 10:53:27.794][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2022-04-12 10:53:27.808][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:27.815][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2022-04-12 10:53:27.817][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:27.820][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2022-04-12 10:53:27.822][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:27.930][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:27.932][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-04-12 10:53:27.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:27.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:27.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:27.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:27.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:27.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:27.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:27.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:27.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:27.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:27.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:27.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:27.994][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:27.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:53:27.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:27.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.001][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:28.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:28.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.008][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:28.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:28.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.016][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:28.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:53:28.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.042][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:28.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:28.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.050][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:28.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:53:28.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.080][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-04-12 10:53:28.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:28.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.088][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-04-12 10:53:28.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:28.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.112][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:28.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:28.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.118][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:28.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:28.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.136][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:28.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:28.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.144][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:28.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:28.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.168][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-04-12 10:53:28.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:28.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.176][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-04-12 10:53:28.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:28.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:28.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:28.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.191][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:28.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:28.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.199][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-04-12 10:53:28.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:28.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.224][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:28.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:28.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.232][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:28.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:28.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.239][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:28.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:28.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:28.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:28.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.254][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:28.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:28.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.278][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:28.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:28.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.286][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:28.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:28.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:28.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:28.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.301][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:28.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:53:28.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:28.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:28.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:28.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:28.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:28.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:28.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:28.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:28.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:28.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:28.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:28.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:28.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:28.368][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2022-04-12 10:53:28.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-04-12 10:53:28.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-04-12 10:53:28.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-04-12 10:53:28.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-04-12 10:53:28.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-04-12 10:53:28.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-04-12 10:53:28.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:53:28.398][biodb::testThat] 
biodb.INFO [2022-04-12 10:53:28.400][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2022-04-12 10:53:28.402][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:28.404][biodb::testThat] 
biodb.TRACE[2022-04-12 10:53:28.409][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:28.412][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:28.414][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.416][ef$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:28.418][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2022-04-12 10:53:28.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:28.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:28.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.484][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:28.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:28.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:28.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:28.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:28.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:28.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:28.502][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-04-12 10:53:28.635][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[2022-04-12 10:53:28.668][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:28.670][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:28.673][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2022-04-12 10:53:29.881][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2022-04-12 10:53:30.719][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:30.757][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2022-04-12 10:53:30.846][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2022-04-12 10:53:30.866][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2022-04-12 10:53:30.891][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:30.893][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:30.895][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:30.897][ef$get] fields variable is a list.
biodb.INFO [2022-04-12 10:53:30.901][biodb::testThat] 
biodb.INFO [2022-04-12 10:53:30.903][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2022-04-12 10:53:30.904][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:30.906][biodb::testThat] 
biodb.TRACE[2022-04-12 10:53:30.935][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:30.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:30.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:30.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:30.942][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:30.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:30.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:30.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:30.950][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:30.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:30.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:30.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:31.215][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-04-12 10:53:31.221][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:31.257][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-04-12 10:53:31.260][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:31.263][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2022-04-12 10:53:31.294][biodb::testThat] 
biodb.INFO [2022-04-12 10:53:31.296][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2022-04-12 10:53:31.298][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:31.299][biodb::testThat] 
biodb.TRACE[2022-04-12 10:53:31.377][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:53:31.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:53:31.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.384][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:53:31.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:53:31.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.392][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-04-12 10:53:31.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-04-12 10:53:31.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.400][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-04-12 10:53:31.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-04-12 10:53:31.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.529][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:53:31.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:53:31.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.538][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:53:31.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:53:31.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.547][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-04-12 10:53:31.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-04-12 10:53:31.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.557][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-04-12 10:53:31.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-04-12 10:53:31.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:53:31.572][biodb::testThat] 
biodb.INFO [2022-04-12 10:53:31.574][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2022-04-12 10:53:31.576][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:31.578][biodb::testThat] 
biodb.INFO [2022-04-12 10:53:31.587][biodb::testThat] 
biodb.INFO [2022-04-12 10:53:31.589][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2022-04-12 10:53:31.591][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:31.593][biodb::testThat] 
biodb.INFO [2022-04-12 10:53:31.602][biodb::testThat] 
biodb.INFO [2022-04-12 10:53:31.604][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2022-04-12 10:53:31.606][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:31.608][biodb::testThat] 
biodb.DEBUG[2022-04-12 10:53:31.615][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2022-04-12 10:53:32.483][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2022-04-12 10:53:32.983][biodb::testThat] 
biodb.INFO [2022-04-12 10:53:32.985][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2022-04-12 10:53:32.987][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:32.989][biodb::testThat] 
biodb.INFO [2022-04-12 10:53:32.998][biodb::testThat] 
biodb.INFO [2022-04-12 10:53:33.000][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2022-04-12 10:53:33.002][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:33.004][biodb::testThat] 
biodb.TRACE[2022-04-12 10:53:33.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:33.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:33.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.034][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:33.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:33.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.040][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:33.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:33.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:33.332][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-04-12 10:53:33.336][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:33.338][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-04-12 10:53:33.341][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:33.342][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2022-04-12 10:53:33.401][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-04-12 10:53:33.407][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:33.410][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-04-12 10:53:33.413][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:33.415][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2022-04-12 10:53:33.450][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:33.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:33.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.465][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:33.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:33.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.499][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:33.611][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2022-04-12 10:53:33.644][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:33.646][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:33.677][private$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[2022-04-12 10:53:38.144][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[2022-04-12 10:53:44.549][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:44.567][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2022-04-12 10:53:44.671][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2022-04-12 10:53:45.362][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[2022-04-12 10:53:45.368][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:45.370][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:45.372][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2022-04-12 10:53:46.074][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2022-04-12 10:53:46.857][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:46.868][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2022-04-12 10:53:46.886][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2022-04-12 10:53:47.008][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2022-04-12 10:53:47.014][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:47.016][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:47.019][private$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[2022-04-12 10:53:47.714][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[2022-04-12 10:53:48.432][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:48.467][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2022-04-12 10:53:48.513][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2022-04-12 10:53:48.554][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-04-12 10:53:48.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-04-12 10:53:48.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:48.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:53:48.570][biodb::testThat] 
biodb.INFO [2022-04-12 10:53:48.571][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2022-04-12 10:53:48.573][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:48.575][biodb::testThat] 
biodb.TRACE[2022-04-12 10:53:48.580][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:48.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:48.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:48.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:48.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:48.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:48.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:48.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:48.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:48.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:48.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:48.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:48.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:48.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:48.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:48.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:48.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:48.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:48.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:48.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:48.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:48.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:48.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:48.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:48.630][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:48.632][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:48.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:48.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.642][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[2022-04-12 10:53:48.969][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[2022-04-12 10:53:48.973][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:48.975][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:48.978][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2022-04-12 10:53:53.687][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2022-04-12 10:54:00.284][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2022-04-12 10:54:00.301][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2022-04-12 10:54:00.321][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2022-04-12 10:54:00.452][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2022-04-12 10:54:00.974][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2022-04-12 10:54:01.148][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-04-12 10:54:01.152][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2022-04-12 10:54:01.154][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2022-04-12 10:54:01.157][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:54:01.159][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:54:01.161][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-04-12 10:54:01.163][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:54:01.165][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:54:01.194][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:54:01.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:54:01.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:54:01.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:54:01.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:54:01.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:54:01.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:54:01.240][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2022-04-12 10:54:01.246][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:01.248][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:01.250][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2022-04-12 10:54:02.038][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2022-04-12 10:54:02.902][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:54:02.938][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2022-04-12 10:54:02.998][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2022-04-12 10:54:03.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:54:03.022][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:54:03.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:54:03.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:54:03.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:54:03.029][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:54:03.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:54:03.032][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2022-04-12 10:54:03.035][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:03.036][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:03.038][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2022-04-12 10:54:03.907][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2022-04-12 10:54:04.723][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:54:04.763][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2022-04-12 10:54:04.824][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2022-04-12 10:54:04.879][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2022-04-12 10:54:04.923][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:54:04.966][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-04-12 10:54:04.968][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-04-12 10:54:04.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:54:04.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:54:04.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:54:04.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:54:04.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:54:04.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:54:04.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:54:04.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:04.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:04.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:04.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:04.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:05.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:05.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:54:05.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:54:05.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:54:05.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:54:05.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.059][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:54:05.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:54:05.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.068][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:54:05.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:54:05.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.074][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:54:05.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:54:05.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.081][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:54:05.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:54:05.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.102][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:54:05.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:54:05.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.109][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:54:05.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:54:05.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.131][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-04-12 10:54:05.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:05.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.139][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-04-12 10:54:05.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:05.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.160][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:54:05.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:54:05.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.168][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:54:05.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:54:05.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.233][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:54:05.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:54:05.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.240][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:54:05.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:54:05.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.265][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-04-12 10:54:05.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:54:05.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.274][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-04-12 10:54:05.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:54:05.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.280][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:54:05.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:54:05.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.288][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:54:05.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:54:05.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.294][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-04-12 10:54:05.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:54:05.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.319][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.326][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:05.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:05.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.342][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:05.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:05.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:05.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:05.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:05.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:05.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:54:05.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:54:05.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:54:05.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:54:05.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:54:05.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:54:05.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:54:05.397][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.TRACE[2022-04-12 10:54:05.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:05.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:05.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:05.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:05.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:54:05.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:54:05.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.446][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:54:05.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:54:05.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.454][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:54:05.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:54:05.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.461][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:54:05.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:54:05.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.469][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:54:05.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:54:05.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.491][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:54:05.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:54:05.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:54:05.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:54:05.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.520][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-04-12 10:54:05.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:05.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.527][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-04-12 10:54:05.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:05.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.569][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:54:05.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:54:05.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.578][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:54:05.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:54:05.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.605][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:54:05.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:54:05.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.614][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:54:05.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:54:05.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.637][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-04-12 10:54:05.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:54:05.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.645][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-04-12 10:54:05.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:54:05.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.651][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:54:05.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:54:05.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.658][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:54:05.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:54:05.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.666][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-04-12 10:54:05.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:54:05.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.691][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.699][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:05.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:05.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.710][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:05.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:05.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:05.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:05.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:05.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:05.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:05.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:05.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:05.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:05.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:05.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:05.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:05.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:05.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:05.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:05.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:05.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:05.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:54:05.798][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2022-04-12 10:54:05.819][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-04-12 10:54:05.822][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:54:05.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:54:05.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:54:05.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:54:05.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:54:05.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:54:05.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:54:05.835][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.844][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.863][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:05.864][private$selectFields] 
biodb.TRACE[2022-04-12 10:54:05.866][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:54:05.867][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:54:05.869][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:05.871][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.874][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.875][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.877][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.879][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.881][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.883][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.885][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.887][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:05.888][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:05.890][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.892][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.894][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.896][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.898][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-04-12 10:54:05.900][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.907][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.913][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.937][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-04-12 10:54:05.939][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:54:05.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:54:05.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:54:05.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:54:05.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:54:05.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:54:05.951][FUN] Functions in observer BiodbConfig: [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[2022-04-12 10:54:05.953][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.959][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.966][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:05.968][private$selectFields] 
biodb.TRACE[2022-04-12 10:54:05.969][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:54:05.971][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:54:05.973][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:05.974][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.976][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.977][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.978][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.979][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.980][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.982][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.983][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.984][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:05.985][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:05.987][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.989][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.990][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.992][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:05.994][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-04-12 10:54:05.995][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:05.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:05.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:06.000][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:06.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:06.007][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:06.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:06.016][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-04-12 10:54:06.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:54:06.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:54:06.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:54:06.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:54:06.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:54:06.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:54:06.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:54:06.032][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:06.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:06.036][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:06.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:06.044][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:06.045][private$selectFields] 
biodb.TRACE[2022-04-12 10:54:06.047][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:54:06.048][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:54:06.050][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:06.052][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.054][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.055][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:06.057][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:06.059][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.061][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.063][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:06.065][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:06.067][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:06.069][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:06.071][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.073][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.074][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:06.076][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:06.078][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-04-12 10:54:06.080][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:06.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:06.087][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:06.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:06.094][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:06.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:06.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:06.100][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-04-12 10:54:06.102][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-04-12 10:54:06.103][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-04-12 10:54:06.119][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-04-12 10:54:06.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-04-12 10:54:06.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:06.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:54:06.129][biodb::testThat] 
biodb.INFO [2022-04-12 10:54:06.131][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2022-04-12 10:54:06.133][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:54:06.134][biodb::testThat] 
biodb.TRACE[2022-04-12 10:54:06.139][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:54:06.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:54:06.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:06.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:06.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:54:06.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:54:06.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:06.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:06.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:06.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:06.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:06.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:06.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:06.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:06.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:06.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:06.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:06.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:06.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:06.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:06.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:06.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:06.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:06.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:54:06.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:54:06.292][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:54:06.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:54:06.298][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:54:06.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:54:06.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:54:06.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:54:06.646][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.INFO [2022-04-12 10:54:06.651][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.DEBUG[2022-04-12 10:54:06.654][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:06.656][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:06.659][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2022-04-12 10:54:11.246][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2022-04-12 10:54:17.588][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:54:17.631][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2022-04-12 10:54:17.781][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2022-04-12 10:54:18.377][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-04-12 10:54:18.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:54:18.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:54:18.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:54:18.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:54:18.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:54:18.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:54:18.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:54:18.473][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.481][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.559][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:18.561][private$selectFields] 
biodb.TRACE[2022-04-12 10:54:18.563][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:54:18.565][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:54:18.567][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:18.570][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.572][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.574][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.576][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.578][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.580][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.582][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.584][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.586][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:18.605][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:18.608][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.610][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.612][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.614][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.616][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-04-12 10:54:18.618][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.624][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.632][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.641][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-04-12 10:54:18.643][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:54:18.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:54:18.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:54:18.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:54:18.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:54:18.652][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:54:18.654][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.TRACE[2022-04-12 10:54:18.656][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.662][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.670][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:18.672][private$selectFields] 
biodb.TRACE[2022-04-12 10:54:18.673][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:54:18.675][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:54:18.676][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:18.678][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.679][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.681][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.683][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.684][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.686][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.687][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.689][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.691][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:18.693][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:18.694][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.696][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.698][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.700][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.702][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-04-12 10:54:18.704][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.712][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.721][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.729][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-04-12 10:54:18.731][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:54:18.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:54:18.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:54:18.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:54:18.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:54:18.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:54:18.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:54:18.744][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.750][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.755][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:18.757][private$selectFields] 
biodb.TRACE[2022-04-12 10:54:18.759][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:54:18.761][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:54:18.763][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:18.765][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.767][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.769][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.770][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.772][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.774][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.776][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.795][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.797][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:18.799][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:18.801][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.803][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.804][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.806][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.807][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-04-12 10:54:18.809][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.815][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.823][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:18.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.831][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-04-12 10:54:18.833][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-04-12 10:54:18.835][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-04-12 10:54:18.851][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-04-12 10:54:18.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-04-12 10:54:18.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:54:18.861][biodb::testThat] 
biodb.INFO [2022-04-12 10:54:18.863][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2022-04-12 10:54:18.865][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:54:18.867][biodb::testThat] 
biodb.TRACE[2022-04-12 10:54:18.873][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:54:18.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:54:18.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:54:18.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:54:18.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:18.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:18.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:18.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:18.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:18.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:18.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:18.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:18.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:54:18.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:18.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:54:18.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:54:18.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:54:18.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:54:18.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:54:18.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:54:18.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:54:18.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:54:19.319][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2022-04-12 10:54:19.325][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:19.327][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:19.329][private$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[2022-04-12 10:54:23.818][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[2022-04-12 10:54:30.109][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:54:30.152][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2022-04-12 10:54:30.288][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2022-04-12 10:54:30.806][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-04-12 10:54:30.808][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:54:30.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:54:30.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:54:30.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:54:30.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:54:30.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:54:30.819][FUN] Functions in observer BiodbConfig: [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[2022-04-12 10:54:30.821][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:30.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:30.830][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:30.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:30.839][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:30.842][private$selectFields] 
biodb.TRACE[2022-04-12 10:54:30.844][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:54:30.846][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:54:30.848][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:30.850][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.852][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.854][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:30.856][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:30.858][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.861][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.863][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:30.865][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:30.867][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:30.869][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:30.871][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.873][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.876][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:30.877][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:30.879][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-04-12 10:54:30.882][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:30.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:30.889][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:30.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:30.898][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:30.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:30.907][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-04-12 10:54:30.909][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:54:30.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:54:30.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:54:30.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:54:30.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:54:30.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:54:30.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:54:30.924][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:30.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:30.932][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:30.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:30.940][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:30.942][private$selectFields] 
biodb.TRACE[2022-04-12 10:54:30.944][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:54:30.946][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:54:30.948][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:30.950][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.952][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.954][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:30.956][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:30.958][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.960][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.962][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:30.964][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:30.966][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:30.968][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:30.970][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.972][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.975][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:30.977][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:30.979][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-04-12 10:54:30.981][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:30.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:31.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:31.006][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:31.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:31.011][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:31.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:31.017][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-04-12 10:54:31.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:54:31.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:54:31.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:54:31.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:54:31.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:54:31.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:54:31.030][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.TRACE[2022-04-12 10:54:31.032][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:31.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:31.040][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:31.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:31.047][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:31.049][private$selectFields] 
biodb.TRACE[2022-04-12 10:54:31.050][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:54:31.052][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:54:31.054][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:31.055][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.057][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.059][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:31.061][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:31.062][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.064][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.066][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:31.068][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:31.070][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:31.072][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:54:31.074][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.075][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.077][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:31.078][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:31.079][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-04-12 10:54:31.080][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:31.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:31.089][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:31.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:31.097][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:31.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:31.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:31.107][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-04-12 10:54:31.109][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-04-12 10:54:31.111][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-04-12 10:54:31.148][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-04-12 10:54:31.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-04-12 10:54:31.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:31.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:54:31.159][biodb::testThat] 
biodb.INFO [2022-04-12 10:54:31.161][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2022-04-12 10:54:31.163][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:54:31.165][biodb::testThat] 
biodb.DEBUG[2022-04-12 10:54:31.169][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2022-04-12 10:54:31.171][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:54:31.175][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2022-04-12 10:54:31.177][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:54:31.179][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:54:31.182][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:54:31.184][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-04-12 10:54:31.186][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:54:31.187][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:54:31.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:54:31.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:54:31.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:54:31.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:54:31.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:54:31.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:54:31.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:54:31.223][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2022-04-12 10:54:31.228][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:31.230][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:31.233][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-04-12 10:54:31.984][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:54:31.986][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:54:31.988][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[2022-04-12 10:54:31.991][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-04-12 10:54:33.136][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-04-12 10:54:33.138][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:33.141][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:33.144][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-04-12 10:54:33.892][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:54:33.894][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:54:33.897][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[2022-04-12 10:54:33.899][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-04-12 10:54:34.747][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-04-12 10:54:34.750][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:34.752][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:34.755][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-04-12 10:54:35.483][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:54:35.485][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:54:35.486][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[2022-04-12 10:54:35.488][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-04-12 10:54:36.675][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-04-12 10:54:36.677][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:36.678][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:36.681][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-04-12 10:54:37.451][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:54:37.453][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:54:37.455][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[2022-04-12 10:54:37.457][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-04-12 10:54:38.979][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-04-12 10:54:38.981][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:38.983][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:38.986][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-04-12 10:54:40.051][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:54:40.053][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:54:40.055][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[2022-04-12 10:54:40.057][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-04-12 10:54:41.261][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-04-12 10:54:41.263][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:41.265][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:41.267][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-04-12 10:54:42.026][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:54:42.028][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:54:42.030][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[2022-04-12 10:54:42.032][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-04-12 10:54:42.958][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-04-12 10:54:42.960][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:42.961][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:42.964][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-04-12 10:54:43.725][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:54:43.727][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:54:43.729][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[2022-04-12 10:54:43.731][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-04-12 10:54:44.577][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-04-12 10:54:44.579][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:44.581][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:44.583][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-04-12 10:54:45.306][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:54:45.307][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:54:45.309][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[2022-04-12 10:54:45.311][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-04-12 10:54:46.471][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-04-12 10:54:46.473][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:46.474][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:46.477][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-04-12 10:54:47.180][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:54:47.181][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:54:47.183][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[2022-04-12 10:54:47.186][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-04-12 10:54:48.243][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-04-12 10:54:48.245][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:48.247][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:48.249][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-04-12 10:54:49.004][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:54:49.006][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:54:49.008][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[2022-04-12 10:54:49.009][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-04-12 10:54:50.049][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2022-04-12 10:54:50.078][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2022-04-12 10:54:50.092][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:54:50.131][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:54:50.132][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-04-12 10:54:50.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:54:50.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:54:50.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:54:50.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:54:50.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:54:50.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:54:50.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:54:50.149][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:50.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:50.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:50.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:50.172][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:50.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:54:50.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:50.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:50.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:50.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:50.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:50.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:50.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:50.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:50.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:50.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:50.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:50.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:50.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:50.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:50.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:50.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:50.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:50.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:50.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:50.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:50.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:50.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:54:50.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:54:50.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:54:50.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:54:50.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:54:50.224][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2022-04-12 10:54:50.226][self$createEntryFromContent] Found %d entry/ies without an accession number. Set it/them to NULL.1
biodb.INFO [2022-04-12 10:54:50.237][biodb::testThat] 
biodb.INFO [2022-04-12 10:54:50.239][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2022-04-12 10:54:50.241][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:54:50.243][biodb::testThat] 
biodb.DEBUG[2022-04-12 10:54:50.257][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2022-04-12 10:54:50.259][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2022-04-12 10:54:50.261][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-04-12 10:54:50.264][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2022-04-12 10:54:50.266][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2022-04-12 10:54:50.268][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:54:50.270][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:54:50.272][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-04-12 10:54:50.274][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:54:50.276][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:54:50.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:54:50.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:54:50.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:54:50.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:54:50.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:54:50.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:54:50.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:54:50.297][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2022-04-12 10:54:50.303][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:50.305][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:50.308][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-04-12 10:54:51.064][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:54:51.066][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:54:51.068][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-04-12 10:54:51.070][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-04-12 10:54:52.079][private$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[2022-04-12 10:54:52.081][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:52.082][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:52.084][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-04-12 10:54:52.816][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:54:52.818][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:54:52.819][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-04-12 10:54:52.821][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-04-12 10:54:53.683][private$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[2022-04-12 10:54:53.685][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:53.686][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:53.688][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-04-12 10:54:54.412][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:54:54.413][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:54:54.416][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-04-12 10:54:54.418][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-04-12 10:54:55.346][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-04-12 10:54:55.348][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:55.350][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:55.353][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-04-12 10:54:56.074][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:54:56.076][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:54:56.078][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-04-12 10:54:56.080][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-04-12 10:54:57.027][private$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[2022-04-12 10:54:57.029][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:57.030][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:57.032][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-04-12 10:54:57.736][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:54:57.737][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:54:57.739][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-04-12 10:54:57.740][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-04-12 10:54:58.564][private$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[2022-04-12 10:54:58.566][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:54:58.568][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:54:58.570][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-04-12 10:54:59.320][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:54:59.321][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:54:59.323][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-04-12 10:54:59.325][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-04-12 10:55:00.481][private$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[2022-04-12 10:55:00.483][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:55:00.484][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:55:00.485][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-04-12 10:55:01.178][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:55:01.180][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:55:01.182][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-04-12 10:55:01.183][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-04-12 10:55:02.320][private$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[2022-04-12 10:55:02.322][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:55:02.327][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:55:02.330][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-04-12 10:55:03.150][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:55:03.152][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:55:03.155][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-04-12 10:55:03.157][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-04-12 10:55:04.182][private$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[2022-04-12 10:55:04.185][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:55:04.187][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:55:04.192][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-04-12 10:55:04.991][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:55:04.993][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:55:04.995][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-04-12 10:55:04.997][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-04-12 10:55:06.186][private$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[2022-04-12 10:55:06.188][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:55:06.191][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:55:06.194][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-04-12 10:55:06.945][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-04-12 10:55:06.947][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-04-12 10:55:06.949][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-04-12 10:55:06.952][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-04-12 10:55:08.014][private$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[2022-04-12 10:55:08.017][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:55:08.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:08.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:08.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:08.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:08.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:08.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:08.032][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2022-04-12 10:55:08.037][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:55:08.039][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:55:08.042][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2022-04-12 10:55:08.826][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2022-04-12 10:55:09.734][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:55:09.773][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2022-04-12 10:55:09.842][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2022-04-12 10:55:09.908][private$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[2022-04-12 10:55:09.938][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:55:09.991][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-04-12 10:55:09.993][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-04-12 10:55:09.996][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:55:10.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:10.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:10.007][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:10.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:10.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:10.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:55:10.018][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:10.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:10.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.027][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:10.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:10.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:10.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:10.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:55:10.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:55:10.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:10.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:10.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:10.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:10.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:10.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:55:10.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:10.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:10.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:10.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:10.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:55:10.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:55:10.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:55:10.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:55:10.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.192][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:55:10.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:55:10.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.203][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:55:10.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:55:10.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.231][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:55:10.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:55:10.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.239][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:55:10.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:55:10.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.275][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:10.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:10.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.285][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:10.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:10.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.316][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:10.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:10.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.329][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:10.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:10.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.365][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-04-12 10:55:10.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:10.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.374][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-04-12 10:55:10.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:10.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.405][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:55:10.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:55:10.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.416][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:55:10.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:55:10.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.446][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:10.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:10.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.456][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:10.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:10.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.512][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-04-12 10:55:10.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:10.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.524][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-04-12 10:55:10.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:10.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.532][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:10.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:10.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.543][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:10.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:10.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.553][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-04-12 10:55:10.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:10.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:10.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:10.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:10.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:10.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.609][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:10.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:10.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.621][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:10.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:10.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.631][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:10.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:10.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.664][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:10.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:10.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.677][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:10.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:10.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:10.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:10.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.701][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:10.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:10.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:10.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:10.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:10.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:10.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:10.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:10.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:10.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:10.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:10.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:10.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:10.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:10.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:10.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:10.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:10.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:10.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:10.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:10.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:10.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:10.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:10.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:10.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:10.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:10.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:55:10.855][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2022-04-12 10:55:10.859][self$createEntryFromContent] Found %d entry/ies without an accession number. Set it/them to NULL.1
biodb.DEBUG[2022-04-12 10:55:10.861][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2022-04-12 10:55:10.926][biodb::testThat] 
biodb.INFO [2022-04-12 10:55:10.928][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2022-04-12 10:55:10.932][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:55:10.934][biodb::testThat] 
biodb.INFO [2022-04-12 10:55:10.994][biodb::testThat] 
biodb.INFO [2022-04-12 10:55:10.997][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2022-04-12 10:55:11.000][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:55:11.004][biodb::testThat] 
biodb.INFO [2022-04-12 10:55:11.019][biodb::testThat] 
biodb.INFO [2022-04-12 10:55:11.021][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2022-04-12 10:55:11.023][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:55:11.029][biodb::testThat] 
biodb.DEBUG[2022-04-12 10:55:11.176][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2022-04-12 10:55:11.183][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:55:11.188][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:55:11.191][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2022-04-12 10:55:15.725][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2022-04-12 10:55:22.325][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:55:22.375][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2022-04-12 10:55:22.552][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.INFO [2022-04-12 10:55:23.253][biodb::testThat] 
biodb.INFO [2022-04-12 10:55:23.255][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2022-04-12 10:55:23.257][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:55:23.259][biodb::testThat] 
biodb.ERROR[2022-04-12 10:55:23.290][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2022-04-12 10:55:23.326][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2022-04-12 10:55:23.350][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-04-12 10:55:23.352][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-04-12 10:55:23.355][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-04-12 10:55:23.357][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-04-12 10:55:23.360][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:23.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:23.364][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:23.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:23.368][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:23.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-04-12 10:55:23.396][biodb::testContext] 
biodb.INFO [2022-04-12 10:55:23.398][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:55:23.400][biodb::testContext] Test context - Web services tests
biodb.INFO [2022-04-12 10:55:23.402][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:55:23.406][biodb::testContext] 
biodb.INFO [2022-04-12 10:55:23.432][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:55:23.435][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-04-12 10:55:23.444][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:55:23.446][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-04-12 10:55:23.485][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-04-12 10:55:23.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:23.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:23.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:23.496][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-04-12 10:55:23.499][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-04-12 10:55:23.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:23.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:23.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:23.508][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-04-12 10:55:23.511][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-04-12 10:55:23.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:23.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:23.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:23.519][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-04-12 10:55:23.521][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-04-12 10:55:23.524][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-04-12 10:55:23.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:23.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:23.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:23.534][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-04-12 10:55:23.536][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-04-12 10:55:23.538][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-04-12 10:55:23.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:23.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:23.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:23.548][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-04-12 10:55:23.552][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-04-12 10:55:23.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:23.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:23.558][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[2022-04-12 10:55:23.560][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-04-12 10:55:23.564][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-04-12 10:55:23.566][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-04-12 10:55:23.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:23.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:23.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:23.575][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-04-12 10:55:23.577][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-04-12 10:55:23.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:23.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:23.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:23.587][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-04-12 10:55:23.589][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-04-12 10:55:23.591][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-04-12 10:55:23.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:23.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:23.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:23.601][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:55:23.604][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-04-12 10:55:23.607][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-04-12 10:55:23.610][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-04-12 10:55:23.612][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-04-12 10:55:23.614][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-04-12 10:55:23.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:23.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:23.620][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[2022-04-12 10:55:23.622][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-04-12 10:55:23.625][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-04-12 10:55:23.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:23.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:23.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:23.637][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-04-12 10:55:23.640][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-04-12 10:55:23.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:23.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:23.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:23.648][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-04-12 10:55:23.650][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-04-12 10:55:23.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:23.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:23.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:23.660][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-04-12 10:55:23.662][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-04-12 10:55:23.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:23.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:23.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:23.671][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-04-12 10:55:23.674][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-04-12 10:55:23.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:23.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:23.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:23.683][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:55:23.686][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-04-12 10:55:23.703][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-04-12 10:55:23.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:23.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:23.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:23.711][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-04-12 10:55:23.714][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-04-12 10:55:23.716][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-04-12 10:55:23.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:23.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:23.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:23.726][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-04-12 10:55:23.730][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:23.732][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-04-12 10:55:23.735][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:23.738][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:55:23.740][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:23.742][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:55:23.744][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:23.748][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:55:23.750][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:55:23.752][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:55:23.754][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:23.758][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-04-12 10:55:23.761][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:55:23.763][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:23.765][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:23.770][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:55:23.770][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:55:23.770][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:55:23.770][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:55:23.770][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:55:23.772][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:55:23.775][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:23.777][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:23.780][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:55:23.782][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:23.784][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:23.786][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:55:23.789][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:23.794][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:55:23.796][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:55:23.798][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:23.800][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:23.803][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-04-12 10:55:23.807][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:23.809][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:55:23.812][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:23.814][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:55:23.817][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:23.819][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:55:23.821][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:23.823][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:55:23.830][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:55:23.832][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:55:23.834][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:23.836][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-04-12 10:55:23.840][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:55:23.842][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:23.844][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:23.846][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:55:23.846][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:55:23.846][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:55:23.846][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:55:23.846][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:55:23.849][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:55:23.852][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:23.854][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:23.856][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:55:23.858][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:23.860][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:23.865][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:55:23.930][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:23.985][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:55:23.988][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:55:23.990][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:23.992][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:23.995][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-04-12 10:55:24.004][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:24.006][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-04-12 10:55:24.008][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:24.010][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:55:24.013][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:24.015][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:55:24.017][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:24.019][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:55:24.021][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:55:24.023][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:55:24.025][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:24.027][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-04-12 10:55:24.029][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:55:24.031][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:24.033][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:24.035][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:24.037][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:55:24.039][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:24.041][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:24.043][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:55:24.045][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:24.047][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:24.049][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:55:24.054][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:24.056][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:55:24.059][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:55:24.061][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:24.063][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:24.068][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-04-12 10:55:24.071][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:24.073][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:55:24.077][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:24.079][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:55:24.081][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:24.083][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:55:24.085][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:24.088][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:55:24.090][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:55:24.093][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:55:24.095][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:24.099][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-04-12 10:55:24.101][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:55:24.103][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:24.106][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:24.108][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:24.113][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:55:24.115][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:24.116][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:24.119][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:55:24.121][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:24.126][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:24.128][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:55:24.130][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:24.133][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:55:24.135][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:55:24.137][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:24.139][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:24.142][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:55:24.144][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.219][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[2022-04-12 10:55:24.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.571][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[2022-04-12 10:55:24.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.607][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-04-12 10:55:24.611][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-04-12 10:55:24.614][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-04-12 10:55:24.617][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-04-12 10:55:24.620][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 10:55:24.623][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-04-12 10:55:24.626][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-04-12 10:55:24.629][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-04-12 10:55:24.632][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-04-12 10:55:24.635][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-04-12 10:55:24.638][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 10:55:24.641][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-04-12 10:55:24.644][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-04-12 10:55:24.647][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-04-12 10:55:24.650][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-04-12 10:55:24.653][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 10:55:24.656][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-04-12 10:55:24.661][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-04-12 10:55:24.663][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 10:55:24.666][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-04-12 10:55:24.670][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-04-12 10:55:24.677][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-04-12 10:55:24.680][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-04-12 10:55:24.683][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-04-12 10:55:24.687][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-04-12 10:55:24.691][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-04-12 10:55:24.694][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-04-12 10:55:24.697][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-04-12 10:55:24.701][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-04-12 10:55:24.704][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-04-12 10:55:24.707][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-04-12 10:55:24.710][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-04-12 10:55:24.714][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-04-12 10:55:24.717][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-04-12 10:55:24.720][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-04-12 10:55:24.723][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-04-12 10:55:24.727][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-04-12 10:55:24.730][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-04-12 10:55:24.734][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-04-12 10:55:24.737][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-04-12 10:55:24.741][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-04-12 10:55:24.744][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-04-12 10:55:24.747][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-04-12 10:55:24.750][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-04-12 10:55:24.753][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-04-12 10:55:24.756][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-04-12 10:55:24.762][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-04-12 10:55:24.765][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-04-12 10:55:24.768][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-04-12 10:55:24.772][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-04-12 10:55:24.775][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-04-12 10:55:24.778][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-04-12 10:55:24.786][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-04-12 10:55:24.789][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-04-12 10:55:24.792][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-04-12 10:55:24.795][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-04-12 10:55:24.800][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-04-12 10:55:24.803][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-04-12 10:55:24.806][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-04-12 10:55:24.811][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-04-12 10:55:24.814][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-04-12 10:55:24.817][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-04-12 10:55:24.821][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-04-12 10:55:24.824][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-04-12 10:55:24.828][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-04-12 10:55:24.832][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-04-12 10:55:24.835][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 10:55:24.838][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 10:55:24.842][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-04-12 10:55:24.845][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-04-12 10:55:24.848][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-04-12 10:55:24.856][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-04-12 10:55:24.859][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-04-12 10:55:24.862][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-04-12 10:55:24.865][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-04-12 10:55:24.870][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-04-12 10:55:24.873][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-04-12 10:55:24.876][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-04-12 10:55:24.881][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-04-12 10:55:24.884][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-04-12 10:55:24.887][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-04-12 10:55:24.890][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-04-12 10:55:24.893][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-04-12 10:55:24.897][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-04-12 10:55:24.902][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:55:24.905][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:55:24.906][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.912][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:24.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:24.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.929][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[2022-04-12 10:55:24.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:24.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:24.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:24.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:24.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:24.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:24.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:24.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:24.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:24.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:25.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:25.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:25.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:25.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:25.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:25.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:25.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:25.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:25.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:25.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:25.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:25.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:25.036][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[2022-04-12 10:55:25.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:25.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:25.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:25.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:25.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:25.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:25.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:25.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:25.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:25.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:25.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:25.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:25.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:25.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:25.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:25.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:25.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:25.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:25.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:25.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:25.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:25.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:25.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:25.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:25.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:25.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:25.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:25.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:25.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:25.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:25.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:25.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:25.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:25.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:25.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:25.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:25.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:25.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:25.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:25.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:25.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:25.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:25.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:25.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:25.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:25.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:25.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:25.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:25.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:25.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:25.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:25.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:25.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:25.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:25.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:25.180][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[2022-04-12 10:55:25.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:25.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:25.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:25.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:25.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:25.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:25.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:25.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:25.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:25.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:25.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:25.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:25.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:25.216][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[2022-04-12 10:55:25.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:25.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:25.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:25.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:25.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:25.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:25.236][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[2022-04-12 10:55:25.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:25.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:25.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:25.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:25.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:25.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:25.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:25.259][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-04-12 10:55:25.264][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-04-12 10:55:25.270][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:25.272][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-04-12 10:55:25.276][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:25.279][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:55:25.281][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:25.284][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:55:25.288][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:25.291][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:55:25.293][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:55:25.296][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:55:25.301][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:25.303][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-04-12 10:55:25.305][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:55:25.308][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-04-12 10:55:25.308][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-04-12 10:55:25.308][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-04-12 10:55:25.308][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-04-12 10:55:25.308][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-04-12 10:55:25.308][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-04-12 10:55:25.308][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-04-12 10:55:25.308][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-04-12 10:55:25.308][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-04-12 10:55:25.311][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:25.313][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:55:25.313][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:55:25.316][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:55:25.320][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:25.324][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:25.326][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:55:25.328][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:25.330][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:25.332][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:55:25.338][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-04-12 10:55:25.338][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-04-12 10:55:25.341][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:55:25.343][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:55:25.345][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:25.348][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:25.351][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-04-12 10:55:25.354][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 10:55:25.365][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-04-12 10:55:25.368][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-04-12 10:55:25.371][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-04-12 10:55:25.374][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-04-12 10:55:25.377][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-04-12 10:55:25.379][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-04-12 10:55:25.382][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-04-12 10:55:25.385][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-04-12 10:55:25.388][biodb::testThat] 
biodb.INFO [2022-04-12 10:55:25.391][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2022-04-12 10:55:25.393][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:55:25.396][biodb::testThat] 
biodb.DEBUG[2022-04-12 10:55:25.592][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[2022-04-12 10:55:25.600][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:55:25.604][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:55:25.606][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2022-04-12 10:55:26.453][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2022-04-12 10:55:27.326][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:55:27.369][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2022-04-12 10:55:27.434][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2022-04-12 10:55:27.691][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2022-04-12 10:55:27.699][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:55:27.702][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:55:27.743][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2022-04-12 10:55:28.565][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[2022-04-12 10:55:29.426][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:55:29.468][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2022-04-12 10:55:29.809][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2022-04-12 10:55:29.847][biodb::testThat] 
biodb.INFO [2022-04-12 10:55:29.849][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2022-04-12 10:55:29.852][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:55:29.854][biodb::testThat] 
biodb.INFO [2022-04-12 10:55:29.896][biodb::testThat] 
biodb.INFO [2022-04-12 10:55:29.899][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2022-04-12 10:55:29.901][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:55:29.903][biodb::testThat] 
biodb.DEBUG[2022-04-12 10:55:30.046][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[2022-04-12 10:55:30.053][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:55:30.055][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:55:30.058][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2022-04-12 10:55:30.682][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2022-04-12 10:55:31.384][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:55:31.425][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2022-04-12 10:55:31.488][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2022-04-12 10:55:31.646][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2022-04-12 10:55:31.653][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:55:31.656][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2022-04-12 10:55:31.658][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:55:31.661][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2022-04-12 10:55:31.787][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2022-04-12 10:55:31.793][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:55:31.795][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:55:31.798][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2022-04-12 10:55:32.423][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[2022-04-12 10:55:33.135][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:55:33.176][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2022-04-12 10:55:33.236][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2022-04-12 10:55:33.376][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[2022-04-12 10:55:33.382][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:55:33.385][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:55:33.389][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2022-04-12 10:55:34.871][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2022-04-12 10:55:37.648][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:55:37.695][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2022-04-12 10:55:37.799][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2022-04-12 10:55:38.040][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2022-04-12 10:55:38.047][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:55:38.050][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:55:38.054][private$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[2022-04-12 10:55:39.603][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[2022-04-12 10:55:41.584][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:55:41.633][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2022-04-12 10:55:41.726][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2022-04-12 10:55:41.844][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-04-12 10:55:41.848][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-04-12 10:55:41.851][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-04-12 10:55:41.856][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-04-12 10:55:41.858][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:41.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:41.862][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:41.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:41.869][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:41.871][FUN] Functions in observer BiodbConfig: [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 [2022-04-12 10:55:41.878][biodb::testContext] 
biodb.INFO [2022-04-12 10:55:41.880][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:55:41.882][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2022-04-12 10:55:41.885][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:55:41.887][biodb::testContext] 
biodb.INFO [2022-04-12 10:55:41.915][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:55:41.920][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-04-12 10:55:41.930][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:55:41.932][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-04-12 10:55:41.937][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-04-12 10:55:41.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:41.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:41.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:41.946][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-04-12 10:55:41.950][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-04-12 10:55:41.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:41.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:41.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:41.960][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-04-12 10:55:41.963][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-04-12 10:55:41.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:41.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:41.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:41.976][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-04-12 10:55:41.978][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-04-12 10:55:41.981][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-04-12 10:55:41.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.013][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-04-12 10:55:42.015][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-04-12 10:55:42.017][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-04-12 10:55:42.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.028][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-04-12 10:55:42.030][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-04-12 10:55:42.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.041][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-04-12 10:55:42.043][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-04-12 10:55:42.047][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-04-12 10:55:42.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.055][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-04-12 10:55:42.060][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-04-12 10:55:42.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.072][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-04-12 10:55:42.075][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-04-12 10:55:42.077][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-04-12 10:55:42.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.088][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:55:42.090][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-04-12 10:55:42.093][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-04-12 10:55:42.099][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-04-12 10:55:42.101][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-04-12 10:55:42.103][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-04-12 10:55:42.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.114][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-04-12 10:55:42.116][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-04-12 10:55:42.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.125][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-04-12 10:55:42.128][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-04-12 10:55:42.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.142][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-04-12 10:55:42.144][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-04-12 10:55:42.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.158][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-04-12 10:55:42.160][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-04-12 10:55:42.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.171][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-04-12 10:55:42.174][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-04-12 10:55:42.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.184][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:55:42.186][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-04-12 10:55:42.203][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-04-12 10:55:42.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.211][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-04-12 10:55:42.215][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-04-12 10:55:42.218][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-04-12 10:55:42.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.227][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-04-12 10:55:42.231][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:42.233][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-04-12 10:55:42.235][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:42.241][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:55:42.244][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:42.246][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:55:42.248][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:42.251][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:55:42.253][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:55:42.255][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:55:42.257][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:42.260][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-04-12 10:55:42.263][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:55:42.266][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:42.268][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:42.269][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:55:42.269][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:55:42.269][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:55:42.269][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:55:42.269][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:55:42.272][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:55:42.277][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:42.280][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:42.282][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:55:42.284][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:42.286][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:42.289][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:55:42.291][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:42.295][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:55:42.297][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:55:42.301][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:42.305][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:42.307][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-04-12 10:55:42.311][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:42.314][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:55:42.316][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:42.318][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:55:42.320][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:42.322][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:55:42.324][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:42.327][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:55:42.329][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:55:42.331][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:55:42.334][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:42.337][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-04-12 10:55:42.339][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:55:42.342][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:42.344][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:42.349][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:55:42.349][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:55:42.349][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:55:42.349][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:55:42.349][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:55:42.351][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:55:42.353][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:42.355][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:42.360][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:55:42.363][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:42.365][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:42.367][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:55:42.369][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:42.373][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:55:42.375][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:55:42.377][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:42.379][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:42.384][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-04-12 10:55:42.387][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:42.389][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-04-12 10:55:42.391][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:42.393][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:55:42.397][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:42.399][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:55:42.402][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:42.404][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:55:42.407][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:55:42.409][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:55:42.411][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:42.414][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-04-12 10:55:42.415][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:55:42.424][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:42.426][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:42.428][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:42.430][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:55:42.435][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:42.437][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:42.439][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:55:42.441][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:42.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:42.445][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:55:42.447][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:42.450][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:55:42.451][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:55:42.453][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:42.456][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:42.459][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-04-12 10:55:42.463][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:42.466][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:55:42.468][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:42.470][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:55:42.475][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:42.477][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:55:42.499][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:42.501][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:55:42.503][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:55:42.507][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:55:42.510][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:42.512][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-04-12 10:55:42.514][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:55:42.517][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:42.520][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:42.523][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:42.527][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:55:42.529][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:42.534][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:42.536][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:55:42.538][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:42.540][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:42.542][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:55:42.547][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:42.549][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:55:42.551][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:55:42.553][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:42.555][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:42.560][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:55:42.562][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.564][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[2022-04-12 10:55:42.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:42.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:42.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:42.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:42.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:42.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:42.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:42.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:42.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:42.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:42.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:42.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:42.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:42.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:42.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:42.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:42.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:42.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:42.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:42.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:42.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.678][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[2022-04-12 10:55:42.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:42.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:42.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:42.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:42.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:42.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:42.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:42.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:42.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:42.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:42.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:42.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:42.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:42.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:42.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:42.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:42.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:42.762][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-04-12 10:55:42.765][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-04-12 10:55:42.768][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-04-12 10:55:42.771][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-04-12 10:55:42.774][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 10:55:42.777][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-04-12 10:55:42.781][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-04-12 10:55:42.786][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-04-12 10:55:42.789][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-04-12 10:55:42.792][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-04-12 10:55:42.800][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 10:55:42.803][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-04-12 10:55:42.806][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-04-12 10:55:42.811][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-04-12 10:55:42.814][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-04-12 10:55:42.816][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 10:55:42.821][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-04-12 10:55:42.824][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-04-12 10:55:42.827][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 10:55:42.832][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-04-12 10:55:42.835][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-04-12 10:55:42.838][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-04-12 10:55:42.841][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-04-12 10:55:42.844][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-04-12 10:55:42.847][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-04-12 10:55:42.850][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-04-12 10:55:42.855][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-04-12 10:55:42.857][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-04-12 10:55:42.861][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-04-12 10:55:42.864][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-04-12 10:55:42.867][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-04-12 10:55:42.870][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-04-12 10:55:42.873][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-04-12 10:55:42.878][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-04-12 10:55:42.881][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-04-12 10:55:42.884][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-04-12 10:55:42.889][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-04-12 10:55:42.892][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-04-12 10:55:42.895][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-04-12 10:55:42.900][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-04-12 10:55:42.904][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-04-12 10:55:42.907][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-04-12 10:55:42.913][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-04-12 10:55:42.916][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-04-12 10:55:42.920][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-04-12 10:55:42.924][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-04-12 10:55:42.941][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-04-12 10:55:42.944][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-04-12 10:55:42.950][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-04-12 10:55:42.953][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-04-12 10:55:42.956][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-04-12 10:55:42.962][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-04-12 10:55:42.965][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-04-12 10:55:42.969][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-04-12 10:55:42.973][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-04-12 10:55:42.976][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-04-12 10:55:42.979][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-04-12 10:55:42.987][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-04-12 10:55:42.990][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-04-12 10:55:42.993][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-04-12 10:55:42.998][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-04-12 10:55:43.002][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-04-12 10:55:43.006][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-04-12 10:55:43.013][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-04-12 10:55:43.016][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-04-12 10:55:43.019][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-04-12 10:55:43.025][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 10:55:43.029][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 10:55:43.032][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-04-12 10:55:43.036][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-04-12 10:55:43.040][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-04-12 10:55:43.043][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-04-12 10:55:43.045][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-04-12 10:55:43.051][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-04-12 10:55:43.054][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-04-12 10:55:43.059][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-04-12 10:55:43.062][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-04-12 10:55:43.065][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-04-12 10:55:43.069][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-04-12 10:55:43.077][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-04-12 10:55:43.079][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-04-12 10:55:43.083][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-04-12 10:55:43.087][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-04-12 10:55:43.090][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-04-12 10:55:43.094][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:55:43.096][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:55:43.101][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:43.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:43.105][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:43.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:43.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:43.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:43.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:43.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:43.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:43.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:43.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:43.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:43.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:43.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:43.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:43.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:43.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:43.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:43.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:43.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:43.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:43.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:43.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:43.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:43.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:43.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:43.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:43.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:43.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:43.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:43.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:43.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:43.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:43.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:43.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:43.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:43.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:43.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:43.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:43.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:43.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:43.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:43.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:43.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:43.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:43.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:43.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:43.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:43.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:43.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:43.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:43.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:43.224][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[2022-04-12 10:55:43.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:43.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:43.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:43.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:43.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:43.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:43.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:43.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:43.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:43.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:43.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:43.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:43.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:43.252][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[2022-04-12 10:55:43.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:43.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:43.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:43.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:43.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:43.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:43.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:43.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:43.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:43.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:43.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:43.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:43.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:43.286][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[2022-04-12 10:55:43.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:43.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:43.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:43.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:43.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:43.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:43.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:43.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:43.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:43.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:43.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:43.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:43.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:43.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:43.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:43.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:43.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:43.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:43.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:43.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:43.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:43.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:43.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:43.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:43.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:43.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:43.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:43.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:43.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:43.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:43.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:43.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:43.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:43.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:43.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:43.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:55:43.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:43.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:43.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:43.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:43.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:43.388][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[2022-04-12 10:55:43.406][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-04-12 10:55:43.409][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-04-12 10:55:43.415][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:43.417][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-04-12 10:55:43.419][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:43.421][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:55:43.425][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:43.428][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:55:43.430][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:43.432][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:55:43.436][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:55:43.438][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:55:43.440][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:43.442][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-04-12 10:55:43.444][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:55:43.448][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-04-12 10:55:43.448][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-04-12 10:55:43.448][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-04-12 10:55:43.448][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-04-12 10:55:43.448][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-04-12 10:55:43.448][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-04-12 10:55:43.448][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-04-12 10:55:43.448][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-04-12 10:55:43.448][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-04-12 10:55:43.451][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-04-12 10:55:43.453][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:55:43.453][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:55:43.455][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:55:43.457][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:43.459][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:43.462][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:55:43.466][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:55:43.468][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:55:43.472][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:55:43.474][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-04-12 10:55:43.474][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-04-12 10:55:43.477][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:55:43.481][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:55:43.487][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-04-12 10:55:43.489][self$setPropertyValue] 
biodb.DEBUG[2022-04-12 10:55:43.492][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-04-12 10:55:43.495][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 10:55:43.501][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-04-12 10:55:43.503][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-04-12 10:55:43.506][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-04-12 10:55:43.509][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-04-12 10:55:43.511][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-04-12 10:55:43.513][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-04-12 10:55:43.515][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-04-12 10:55:43.518][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-04-12 10:55:43.520][biodb::testThat] 
biodb.INFO [2022-04-12 10:55:43.523][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2022-04-12 10:55:43.525][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:55:43.527][biodb::testThat] 
biodb.DEBUG[2022-04-12 10:55:43.660][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[2022-04-12 10:55:43.668][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:55:43.672][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2022-04-12 10:55:43.675][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:55:43.731][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2022-04-12 10:55:45.242][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2022-04-12 10:55:45.244][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-04-12 10:55:45.248][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2022-04-12 10:55:45.250][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2022-04-12 10:55:45.252][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:55:45.255][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:55:45.258][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-04-12 10:55:45.260][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:55:45.262][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:55:45.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:55:45.272][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:45.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:45.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:45.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:45.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:45.286][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[2022-04-12 10:55:45.288][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2022-04-12 10:55:45.296][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:55:45.298][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:55:45.301][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2022-04-12 10:55:46.163][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.DEBUG[2022-04-12 10:55:47.021][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:55:47.085][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.content"
biodb.TRACE[2022-04-12 10:55:47.147][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.request"
biodb.DEBUG[2022-04-12 10:55:47.169][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:55:47.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:47.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:47.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:47.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:47.190][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:47.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:55:47.194][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2022-04-12 10:55:47.203][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:55:47.206][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:55:47.209][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2022-04-12 10:55:47.996][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2022-04-12 10:55:48.885][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:55:48.933][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2022-04-12 10:55:49.002][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.TRACE[2022-04-12 10:55:49.077][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv"
biodb.DEBUG[2022-04-12 10:55:49.105][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:55:49.184][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-04-12 10:55:49.186][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-04-12 10:55:49.191][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:55:49.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:49.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:49.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:49.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:49.202][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:49.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:55:49.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:49.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:49.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:49.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:49.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:55:49.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:55:49.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.266][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:55:49.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:55:49.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.280][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:55:49.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:55:49.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.291][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:49.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:49.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.303][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:49.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:49.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.337][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:49.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:49.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.348][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:49.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:49.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.380][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-04-12 10:55:49.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:49.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.392][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-04-12 10:55:49.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:49.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.424][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:55:49.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:55:49.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.433][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:55:49.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:55:49.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.465][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:49.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:49.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.476][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:49.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:49.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.508][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-04-12 10:55:49.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:49.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.518][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-04-12 10:55:49.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:49.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.550][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:49.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:49.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:49.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:49.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.568][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-04-12 10:55:49.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:49.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.606][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:49.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:49.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:49.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:49.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.627][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:49.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:49.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.637][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:49.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:49.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.647][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:49.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:49.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.679][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:49.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:49.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.690][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:49.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:49.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:49.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:49.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.710][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:49.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:49.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:49.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:49.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:49.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:49.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:49.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:49.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:55:49.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:55:49.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:49.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:49.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:49.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:49.791][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:49.793][FUN] Functions in observer BiodbConfig: [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[2022-04-12 10:55:49.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:49.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:49.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:49.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:49.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:55:49.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:55:49.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.861][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:55:49.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:55:49.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.896][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:55:49.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-04-12 10:55:49.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.908][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:55:49.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:55:49.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.916][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:49.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:49.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.926][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:49.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:49.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.976][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:49.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:49.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:49.986][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:49.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:49.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:49.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.015][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-04-12 10:55:50.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:50.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.026][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-04-12 10:55:50.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:50.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.057][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:55:50.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:55:50.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.066][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:55:50.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:55:50.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:50.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:50.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.114][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:50.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:50.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.147][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-04-12 10:55:50.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:50.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.156][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-04-12 10:55:50.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:50.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.165][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:50.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:50.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.176][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:50.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:50.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.189][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-04-12 10:55:50.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:50.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.223][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:50.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:50.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.236][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:50.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:50.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:50.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:50.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.256][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:50.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:50.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:50.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:50.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:50.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:50.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:50.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:50.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:50.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:50.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:50.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:50.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:50.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:50.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:50.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:50.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:50.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:50.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:50.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:50.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:55:50.400][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2022-04-12 10:55:50.404][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2022-04-12 10:55:50.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:55:50.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:50.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:50.415][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:50.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:50.420][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:50.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:55:50.425][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:55:50.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:55:50.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.437][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:55:50.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:55:50.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.449][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-04-12 10:55:50.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-04-12 10:55:50.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.460][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-04-12 10:55:50.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-04-12 10:55:50.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.473][private$selectFields] Fields none
biodb.TRACE[2022-04-12 10:55:50.475][private$selectFields] 
biodb.TRACE[2022-04-12 10:55:50.478][private$selectFields] Fields is null: TRUE
biodb.TRACE[2022-04-12 10:55:50.480][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:55:50.484][private$selectFields] Fields [7]: "accession, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:55:50.486][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:50.488][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:50.490][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.494][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.496][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:50.499][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:50.501][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.503][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.507][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:50.509][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:50.511][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.513][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.515][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:50.520][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:50.522][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.524][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.526][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:55:50.531][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:55:50.533][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.535][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.537][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:50.539][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:50.543][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.545][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.547][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:50.549][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:50.551][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.553][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.555][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:50.557][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:50.559][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.561][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.564][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:50.566][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:50.569][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.571][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.575][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:50.577][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:50.579][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.581][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.583][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:50.585][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:50.587][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.590][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.592][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:55:50.594][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:55:50.597][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.599][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.601][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:50.603][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:50.606][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.608][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.610][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:50.612][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:50.614][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.617][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.619][private$selectFields] Fields [7]: "accession, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:55:50.621][private$organizeFieldsByGroups] Fields [7]: "accession, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:55:50.624][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:50.626][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:50.630][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.632][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.634][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:50.637][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:50.641][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.643][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.645][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:50.647][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:50.649][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.653][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.655][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:50.658][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:50.661][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.665][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.668][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:55:50.670][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:55:50.672][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.674][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.676][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:50.678][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:50.680][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.683][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.685][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:50.690][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:50.692][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.694][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.696][private$organizeFieldsByGroups] Groups [2]: "c("accession", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2022-04-12 10:55:50.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:50.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:50.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:50.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:50.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:50.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:50.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.732][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:50.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:50.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.745][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:50.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:50.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.778][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:50.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:50.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.788][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:50.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:50.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.799][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:50.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:50.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.807][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:50.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:50.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:50.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:50.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:50.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:50.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:50.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:50.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.852][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:55:50.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:55:50.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.862][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:55:50.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:55:50.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.870][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:55:50.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:55:50.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.878][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:50.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:50.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.887][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:50.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:50.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.896][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:50.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:50.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.906][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:50.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:50.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.915][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:50.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:50.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.925][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:50.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:50.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.947][private$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[2022-04-12 10:55:50.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:55:50.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:50.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:50.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:50.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:50.961][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:50.963][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.TRACE[2022-04-12 10:55:50.968][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:55:50.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:55:50.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.978][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:55:50.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:55:50.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.987][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-04-12 10:55:50.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-04-12 10:55:50.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:50.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:50.996][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-04-12 10:55:50.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-04-12 10:55:51.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.005][private$selectFields] Fields none
biodb.TRACE[2022-04-12 10:55:51.007][private$selectFields] 
biodb.TRACE[2022-04-12 10:55:51.012][private$selectFields] Fields is null: TRUE
biodb.TRACE[2022-04-12 10:55:51.014][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:55:51.016][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:55:51.018][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:51.021][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:51.023][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.025][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.027][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:55:51.030][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:55:51.033][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.035][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.037][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:51.039][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:51.041][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.047][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.049][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:51.051][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:51.053][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.057][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.059][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:51.061][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:51.063][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.065][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.072][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:55:51.074][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:55:51.076][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.078][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.086][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:51.089][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:51.091][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.093][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.095][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:51.099][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:51.101][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.103][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.105][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:51.107][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:51.111][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.113][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.115][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:55:51.117][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:55:51.119][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.123][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.125][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:51.128][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:51.130][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.134][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.136][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:51.138][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:51.140][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.143][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.148][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:51.151][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:51.153][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.155][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.183][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:55:51.186][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:55:51.188][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.190][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.192][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:51.198][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:51.200][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.202][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.205][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:51.210][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:51.212][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.214][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.216][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:55:51.218][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-04-12 10:55:51.221][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:51.223][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:51.225][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.227][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.229][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:55:51.232][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:55:51.234][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.235][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.237][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:51.240][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:51.243][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.245][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.248][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:51.251][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:51.254][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.256][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.258][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:51.260][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:51.263][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.266][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.268][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:55:51.270][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:55:51.273][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.277][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.279][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:51.281][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:51.283][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.285][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.291][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:51.293][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:51.295][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.297][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.303][private$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[2022-04-12 10:55:51.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:51.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:51.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:51.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:51.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:55:51.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:55:51.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.338][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:55:51.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:55:51.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:55:51.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:55:51.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:55:51.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:55:51.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.374][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:51.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:51.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.384][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:51.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:51.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.395][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:51.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-04-12 10:55:51.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.405][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:51.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:51.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.415][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:51.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:51.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.425][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:51.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-04-12 10:55:51.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:51.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:51.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:51.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:51.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:51.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:55:51.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.474][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:55:51.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:55:51.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.488][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:55:51.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:55:51.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.502][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:55:51.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:55:51.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.513][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:51.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:51.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.523][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:51.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:51.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.534][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:55:51.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:55:51.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.544][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:51.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:51.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.554][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:51.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:51.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.566][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:51.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-04-12 10:55:51.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:55:51.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:55:51.585][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2022-04-12 10:55:51.611][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2022-04-12 10:55:51.613][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2022-04-12 10:55:51.619][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-04-12 10:55:51.623][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-04-12 10:55:51.626][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-04-12 10:55:51.628][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-04-12 10:55:51.630][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:55:51.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:55:51.635][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:55:51.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:55:51.639][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:55:51.641][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 170 ]
> 
> proc.time()
   user  system elapsed 
 45.969   2.475 150.193

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn3.3700.5853.964
LipidmapsStructureEntry0.7170.0210.739